Document and Entity Information - shares shares in Millions	9 Months Ended
Document and Entity Information - shares shares in Millions	Oct. 02, 2016	Oct. 21, 2016
Document and Entity Information [Abstract]
Entity Registrant Name	Illumina Inc
Entity Central Index Key	0001110803
Current Fiscal Year End Date	--01-03
Entity Filer Category	Large Accelerated Filer
Document Type	10-Q
Document Period End Date	Oct. 02, 2016
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	Q3
Amendment Flag	false
Entity Common Stock, Shares Outstanding		146.9

Condensed Consolidated Balance Sheets (Unaudited) - USD ($) $ in Thousands	Oct. 02, 2016	Jan. 03, 2016
Current assets:
Cash and cash equivalents	$ 794,697	$ 768,770
Short-term investments	741,569	617,450
Accounts receivable, net	381,632	385,529
Inventory	312,242	270,777
Prepaid expenses and other current assets	47,696	54,297
Total current assets	2,277,836	2,096,823
Property and equipment, net	633,856	342,694
Goodwill	775,995	752,629
Intangible assets, net	255,560	273,621
Deferred tax assets	182,122	134,515
Other assets	102,458	87,465
Total assets	4,227,827	3,687,747
Current liabilities:
Accounts payable	134,090	139,226
Accrued liabilities	315,204	386,844
Build-to-suit lease liability	178,311	9,495
Long-term debt, current portion	1,250	74,929
Total current liabilities	628,855	610,494
Long-term debt	1,040,765	1,015,649
Other long-term liabilities	204,273	180,505
Redeemable noncontrolling interests	34,257	32,546
Stockholders’ equity:
Common stock	1,882	1,859
Additional paid-in capital	2,738,001	2,497,501
Accumulated other comprehensive income	1,314	36
Retained earnings	1,361,652	1,022,765
Treasury stock, at cost	(1,862,702)	(1,673,608)
Total Illumina stockholders' equity	2,240,147	1,848,553
Noncontrolling interests	79,530
Total stockholders’ equity	2,319,677	1,848,553
Total liabilities and stockholders’ equity	$ 4,227,827	$ 3,687,747

Condensed Consolidated Statements of Income (Unaudited) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Oct. 02, 2016	Sep. 27, 2015	Oct. 02, 2016	Sep. 27, 2015
Revenue:
Product revenue	$ 513,744	$ 470,824	$ 1,506,416	$ 1,392,711
Service and other revenue	93,395	79,447	272,610	235,503
Total revenue	607,139	550,271	1,779,026	1,628,214
Cost of revenue:
Cost of product revenue	132,423	120,954	382,856	360,037
Cost of service and other revenue	37,606	29,590	117,156	94,289
Amortization of acquired intangible assets	10,960	12,188	32,005	34,957
Total cost of revenue	180,989	162,732	532,017	489,283
Gross profit	426,150	387,539	1,247,009	1,138,931
Operating expense:
Research and development	125,917	99,226	374,500	287,180
Selling, general and administrative	139,146	136,648	436,914	377,406
Legal contingencies		15,000	(9,490)	15,000
Headquarter relocation	385	(5,226)	1,069	(3,047)
Acquisition related expense (gain), net		1,109		(6,449)
Total operating expense	265,448	246,757	802,993	670,090
Income from operations	160,702	140,782	444,016	468,841
Other income (expense):
Interest income	2,056	2,767	6,683	5,804
Interest expense	(8,208)	(12,821)	(24,880)	(35,190)
Cost-method investment gain, net		2,900		15,482
Other (expense) income, net	(186)	(4,711)	1,116	(6,802)
Total other expense, net	(6,338)	(11,865)	(17,081)	(20,706)
Income before income taxes	154,364	128,917	426,935	448,135
Provision for income taxes	37,429	13,296	106,387	93,609
Consolidated net income	116,935	115,621	320,548	354,526
Add: Net loss attributable to noncontrolling interests	11,953	2,556	18,339	2,556
Net income attributable to Illumina stockholders	128,888	118,177	338,887	357,082
Net income attributable to Illumina stockholders for earnings per share	$ 128,682	$ 118,128	$ 335,597	$ 357,033
Earnings per share attributable to Illumina stockholders:
Basic (in dollars per share)	$ 0.88	$ 0.81	$ 2.29	$ 2.47
Diluted (in dollars per share)	$ 0.87	$ 0.79	$ 2.27	$ 2.39
Shares used in computing earnings per common share:
Basic (in shares)	146,705	145,349	146,783	144,447
Diluted (in shares)	147,901	149,672	148,049	149,108

Condensed Consolidated Statements of Comprehensive Income (Unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Oct. 02, 2016	Sep. 27, 2015	Oct. 02, 2016	Sep. 27, 2015
Statement of Comprehensive Income [Abstract]
Consolidated net income	$ 116,935	$ 115,621	$ 320,548	$ 354,526
Unrealized (loss) gain on available-for-sale securities, net of deferred tax	(1,004)	441	1,278	2,120
Total consolidated comprehensive income	115,931	116,062	321,826	356,646
Add: Comprehensive loss attributable to noncontrolling interests	11,953	2,556	18,339	2,556
Comprehensive income attributable to Illumina stockholders	$ 127,884	$ 118,618	$ 340,165	$ 359,202

Condensed Consolidated Statement of Stockholders' Equity Statement - 9 months ended Oct. 02, 2016 - USD ($) $ in Thousands	Total	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Other Comprehensive Income [Member]	Retained Earnings [Member]	Treasury Stock [Member]	Noncontrolling Interests [Member]
Beginning balance at Jan. 03, 2016	$ 1,848,553	$ 1,859	$ 2,497,501	$ 36	$ 1,022,765	$ (1,673,608)	$ 0
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss)	332,340				338,887		(6,547)
Unrealized gain on available-for-sale securities, net of deferred tax	1,278			1,278
Issuance of common stock, net of repurchases	(142,302)	23	47,115			(189,440)
Tax impact from the conversion of convertible notes	36		36
Share-based compensation	101,494		101,494
Net incremental tax benefit related to share-based compensation	109,292		109,292
Adjustment to the carrying value of redeemable noncontrolling interests	(12,023)		(12,023)
Vesting of redeemable equity awards	(1,481)		(1,481)
Vesting of non-redeemable equity awards	0		(28)				28
Issuance of subsidiary shares in business combination	2,300		2,102				198
Issuance of treasury stock	3,900		3,554			346
Contributions from noncontrolling interest owners	80,000						80,000
Proceeds from early exercise of equity awards from a subsidiary	5,851						5,851
Tax impact of deemed dividend from GRAIL, Inc.	(9,561)		(9,561)
Ending balance at Oct. 02, 2016	$ 2,319,677	$ 1,882	$ 2,738,001	$ 1,314	$ 1,361,652	$ (1,862,702)	$ 79,530

Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	9 Months Ended
	Oct. 02, 2016	Sep. 27, 2015
Cash flows from operating activities:
Consolidated net income	$ 320,548	$ 354,526
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation expense	65,433	52,774
Amortization of intangible assets	38,051	40,884
Share-based compensation expense	101,845	97,104
Accretion of debt discount	22,342	29,828
Incremental tax benefit related to share-based compensation	(109,934)	(121,703)
Deferred income tax expense	57,539	83,679
Cost-method investment gain, net		(15,482)
Change in fair value of contingent consideration		(6,449)
Other	5,190	6,178
Changes in operating assets and liabilities:
Accounts receivable	4,999	(121,309)
Inventory	(41,757)	(43,598)
Prepaid expenses and other current assets	3,572	(4,982)
Other assets	(6,060)	(428)
Accounts payable	(7,307)	49,532
Accrued liabilities	(57,325)	23,884
Other long-term liabilities	9,949	(5,220)
Net cash provided by operating activities	407,085	419,218
Cash flows from investing activities:
Purchases of available-for-sale securities	(679,064)	(713,862)
Sales of available-for-sale securities	406,286	335,351
Maturities of available-for-sale securities	148,290	189,929
Net cash paid for acquisitions	(17,841)	(35,226)
Net purchases of strategic investments	9,075	4,100
Purchases of property and equipment	(178,353)	(107,361)
Cash paid for intangible assets	11,490	275
Net cash used in investing activities	(341,247)	(335,544)
Cash flows from financing activities:
Payments on financing obligations	(70,522)	(216,207)
Payments on acquisition related contingent consideration liability	(29,200)	(1,500)
Proceeds from issuance of debt	5,000
Incremental tax benefit related to share-based compensation	109,934	121,703
Common stock repurchases	(113,075)	(72,256)
Taxes paid related to net share settlement of equity awards	(76,365)	(95,157)
Proceeds from issuance of common stock	47,156	65,668
Proceeds from early exercise of equity awards from a subsidiary	5,851
Contributions from noncontrolling interest owners	80,000	32,128
Net cash used in financing activities	(41,221)	(165,621)
Effect of exchange rate changes on cash and cash equivalents	1,310	(2,678)
Net increase (decrease) in cash and cash equivalents	25,927	(84,625)
Cash and cash equivalents at beginning of period	768,770	636,154
Cash and cash equivalents at end of period	$ 794,697	$ 551,529

Basis of Presentation and Summary of Significant Accounting Policies

9 Months Ended

Oct. 02, 2016

Accounting Policies [Abstract]

Basis of Presentation and Summary of Significant Accounting Policies

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (GAAP) for interim financial information and the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. Interim financial results are not necessarily indicative of results anticipated for the full year. These unaudited condensed consolidated financial statements should be read in conjunction with the Company’s audited consolidated financial statements and footnotes included in the Company’s Annual Report on Form 10-K for the fiscal year ended January 3, 2016, from which the balance sheet information herein was derived. The preparation of financial statements requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue, and expense, and related disclosure of contingent assets and liabilities. Actual results could differ from those estimates.

The unaudited condensed consolidated financial statements include the accounts of the Company, its wholly-owned subsidiaries, majority-owned or controlled companies, and variable interest entities (VIEs) for which the Company is the primary beneficiary. All intercompany transactions and balances have been eliminated in consolidation. In management’s opinion, the accompanying financial statements reflect all adjustments, consisting of normal recurring adjustments, considered necessary for a fair presentation of the results for the interim periods presented.

The Company evaluates its ownership, contractual and other interests in entities that are not wholly-owned by the Company to determine if these entities are VIEs, and, if so, whether the Company is the primary beneficiary of the VIE. In determining whether the Company is the primary beneficiary of a VIE and is therefore required to consolidate the VIE, the Company applies a qualitative approach that determines whether it has both (1) the power to direct the activities of the VIE that most significantly impact the VIE’s economic performance and (2) the obligation to absorb losses of, or the rights to receive benefits from, the VIE that could potentially be significant to that VIE. The Company continuously assesses whether it is the primary beneficiary of a VIE as changes to existing relationships or future transactions may result in the consolidation or deconsolidation, as the case may be. The Company has not provided financial or other support during the periods presented to its VIEs that it was not previously contractually required to provide.

The equity method is used to account for investments in which the Company has the ability to exercise significant influence, but not control, over the investee. Such investments are recorded within other assets, and the share of net income or losses of equity investments is recognized on a one quarter lag in other (expense) income, net.

Segment Information

The Company is organized into three operating segments for purposes of evaluating its business operations and reporting its financial results. One operating segment consists of Illumina’s core operations and the other two relate to the Company’s consolidated VIEs. The combined results of operations of the Company’s consolidated VIEs became material for the three and nine months ended October 2, 2016. As such, the Company commenced reporting two segments in the third quarter of 2016. Financial information for all periods presented has been classified to reflect these changes to our reportable segments. For further information on the Company’s segments, refer to note “9. Segment Information”.

Fiscal Year

The Company’s fiscal year consists of 52 or 53 weeks ending the Sunday closest to December 31, with quarters of 13 or 14 weeks ending the Sunday closest to March 31, June 30, September 30, and December 31. The three and nine months ended October 2, 2016 and September 27, 2015 were both 13 and 39 weeks, respectively.

Reclassifications

Certain prior period amounts have been reclassified to conform to the current period presentation.

Significant Accounting Policies

During the three and nine months ended October 2, 2016, there have been no changes to the Company’s significant accounting policies as described in the Annual Report on Form 10-K for the fiscal year ended January 3, 2016.

Recent Accounting Pronouncements

In March 2016, the Financial Accounting Standards Board issued Accounting Standard Update (ASU) 2016-09, Compensation - Stock Compensation (Topic 718). The new standard requires income tax effects of stock compensation awards to be recognized in the income statement when the awards vest or are settled. The new standard also allows the Company to repurchase more of an employee’s shares for tax withholding purposes without triggering liability accounting and to make a policy election to account for forfeitures as they occur. ASU 2016-09 will be effective for the Company beginning in the first quarter of 2017. The Company is currently evaluating the impact of ASU 2016-09 on its consolidated financial statements.

In February 2016, the Financial Accounting Standards Board issued ASU 2016-02, Leases (Topic 842). The new standard requires lessees to recognize most leases on their balance sheets as lease liabilities with corresponding right-of-use assets and eliminates certain real estate-specific provisions. ASU 2016-02 will be effective for the Company beginning in the first quarter of 2019. ASU 2016-02 will be adopted on a modified retrospective transition basis for leases existing at, or entered into after, the beginning of the earliest comparative period presented in the financial statements. The Company is currently evaluating the impact of ASU 2016-02 on its consolidated financial statements.

In May 2014, the Financial Accounting Standards Board issued ASU 2014-09, Revenue from Contracts with Customers (Topic 606). The new standard is based on the principle that revenue should be recognized to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. ASU 2014-09 will be effective for the Company beginning in the first quarter of 2018 and allows for a full retrospective or a modified retrospective adoption approach. The Company is currently evaluating the impact of ASU 2014-09 on its consolidated financial statements.

Earnings per Share

Basic earnings per share attributable to Illumina stockholders is computed based on the weighted average number of common shares outstanding during the period. Diluted earnings per share attributable to Illumina stockholders is computed based on the sum of the weighted average number of common shares and potentially dilutive common shares outstanding during the period. Per-share earnings of our VIEs are included in the Company’s consolidated basic and diluted earnings per share computations based on the Company’s share of the VIE’s securities.

Potentially dilutive common shares consist of shares issuable under convertible senior notes, equity awards, and warrants. Convertible senior notes have a dilutive impact when the average market price of the Company’s common stock exceeds the applicable conversion price of the respective notes. Potentially dilutive common shares from equity awards and warrants are determined using the average share price for each period under the treasury stock method. In addition, the following amounts are assumed to be used to repurchase shares: proceeds from exercise of equity awards and warrants; the average amount of unrecognized compensation expense for equity awards; and estimated tax benefits that will be recorded in additional paid-in capital when expenses related to equity awards become deductible. In loss periods, basic net loss per share and diluted net loss per share are identical because the otherwise dilutive potential common shares become anti-dilutive and are therefore excluded.

The following table presents the calculation of weighted average shares used to calculate basic and diluted earnings per share (in thousands):



	Three Months Ended		Nine Months Ended
	October 2, 2016	September 27, 2015	October 2, 2016	September 27, 2015
Weighted average shares outstanding	146,705	145,349	146,783	144,447
Effect of potentially dilutive common shares from:
Convertible senior notes	—	1,670	80	2,013
Equity awards	1,196	2,653	1,186	2,648
Weighted average shares used in calculating diluted earnings per share	147,901	149,672	148,049	149,108
Potentially dilutive shares excluded from calculation due to anti-dilutive effect	63	13	580	7

Balance Sheet Account Details

9 Months Ended

Oct. 02, 2016

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Balance Sheet Account Details

Short-Term Investments

The following is a summary of short-term investments (in thousands):



	October 2, 2016									January 3, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Available-for-sale securities:
Debt securities in government sponsored entities	$	29,687	$	—	$	(30	)	$	29,657	$	14,634	$	—	$	(8	)	$	14,626
Corporate debt securities	463,484		282		(474		)	463,292		422,177		44		(1,127		)	421,094
U.S. Treasury securities	248,542		182		(104		)	248,620		182,144		3		(417		)	181,730
Total available-for-sale securities	$	741,713	$	464	$	(608	)	$	741,569	$	618,955	$	47	$	(1,552	)	$	617,450

Realized gains and losses are determined based on the specific identification method and are reported in interest income.

Contractual maturities of available-for-sale debt securities as of October 2, 2016 were as follows (in thousands):



	Estimated Fair Value
Due within one year	$	279,548
After one but within five years	462,021
Total	$	741,569

The Company has the ability, if necessary, to liquidate any of its cash equivalents and short-term investments in order to meet its liquidity needs in the next 12 months. Accordingly, those investments with contractual maturities greater than one year from the date of purchase nonetheless are classified as short-term on the accompanying condensed consolidated balance sheets.

Strategic Investments

As of October 2, 2016 and January 3, 2016, the aggregate carrying amounts of the Company’s cost-method investments in non-publicly traded companies included in other assets were $56.9 million and $56.6 million, respectively. Revenue recognized from transactions with such companies was $12.5 million and $42.1 million, respectively, for the three and nine months ended October 2, 2016 and $16.1 million and $47.3 million, respectively, for the three and nine months ended September 27, 2015.

During the nine months ended September 27, 2015, the Company recognized a gain on a disposition of a cost-method investment of $18.0 million. The Company’s cost-method investments are assessed for impairment quarterly. The Company determines that it is not practicable to estimate the fair value of its cost-method investments on a regular basis and does not reassess the fair value of cost-method investments if there are no identified events or changes in circumstances that may have a significant adverse effect on the fair value of the investments. No material impairment loss was recorded during the three and nine months ended October 2, 2016 or September 27, 2015.

On April 14, 2016, the Company announced that it has committed to invest $100.0 million in a new venture capital investment fund (the Fund). The capital commitment is callable over ten years, and up to $40.0 million can be drawn down during the first year. The Company’s investment in the Fund is accounted for as an equity method investment. During the nine months ended October 2, 2016, the Company transferred $3.2 million of its cost-method investments to the Fund and contributed $4.4 million in cash.

Inventory

Inventory consists of the following (in thousands):



	October 2, 2016		January 3, 2016
Raw materials	$	101,646	$	97,740
Work in process	166,050		138,322
Finished goods	44,546		34,715
Total inventory	$	312,242	$	270,777

Property and Equipment

Property and equipment, net consists of the following (in thousands):



	October 2, 2016			January 3, 2016
Leasehold improvements	$	197,534		$	178,019
Machinery and equipment	264,556			224,158
Computer hardware and software	153,851			136,550
Furniture and fixtures	20,448			18,539
Building	7,670			7,670
Construction in progress	308,825			44,501
Total property and equipment, gross	952,884			609,437
Accumulated depreciation	(319,028		)	(266,743		)
Total property and equipment, net	$	633,856		$	342,694

Property and equipment, net included accrued expenditures of $194.4 million for the nine months ended October 2, 2016, which includes $168.8 million in construction in progress recorded under build-to-suit lease accounting. Accrued capital expenditures were excluded from the condensed consolidated statements of cash flows. Accrued capital expenditures were immaterial for the nine months ended September 27, 2015.

Goodwill

The Company tests the carrying value of goodwill in accordance with accounting rules on impairment of goodwill, which require the Company to estimate the fair value of the reporting units annually, or when impairment indicators exist, and compare such amounts to their respective carrying values to determine if an impairment is required. The Company performed its annual assessment for goodwill impairment in the second quarter of 2016, noting no impairment.

Changes in the Company’s goodwill balance during the nine months ended October 2, 2016 are as follows (in thousands):



	Goodwill
Balance as of January 3, 2016	$	752,629
Current period acquisitions	23,366
Balance as of October 2, 2016	$	775,995

In January 2016, the Company closed two acquisitions consisting of $17.8 million in upfront cash payments, equity instruments, and certain contingent consideration provisions.

Derivatives

The Company is exposed to foreign exchange rate risks in the normal course of business. The Company enters into foreign exchange contracts to manage foreign currency risks related to monetary assets and liabilities that are denominated in currencies other than the U.S. dollar. These foreign exchange contracts are carried at fair value in other assets or other liabilities and are not designated as hedging instruments. Changes in the value of the derivative are recognized in other expense, net, along with the remeasurement gain or loss on the foreign currency denominated assets or liabilities.

As of October 2, 2016, the Company had foreign exchange forward contracts in place to hedge exposures in the euro, Japanese yen, and Australian dollar. As of October 2, 2016 and January 3, 2016, the total notional amounts of outstanding forward contracts in place for foreign currency purchases were $62.2 million and $61.3 million, respectively.

Accrued Liabilities

Accrued liabilities consist of the following (in thousands):



	October 2, 2016		January 3, 2016
Deferred revenue, current portion	$	116,118	$	96,654
Accrued compensation expenses	89,527		120,662
Accrued taxes payable	30,855		44,159
Customer deposits	17,831		20,901
Acquisition related contingent liability, current portion	7,220		35,000
Other	53,653		69,468
Total accrued liabilities	$	315,204	$	386,844

Build-to-Suit Lease Liability

The Company evaluates whether it is the accounting owner during the construction period when the Company is involved in the construction of leased assets. As a result, the Company is considered the owner of three construction projects for accounting purposes only under build-to-suit lease accounting due to certain indemnification obligations related to the construction. As of October 3, 2016 and January 3, 2016, the Company has recorded $178.3 million and $9.5 million, respectively, in project construction costs incurred by the landlord as construction in progress and a corresponding build-to-suit lease liability. Once the landlord completes the construction projects, the Company will evaluate the lease in order to determine whether or not it meets the criteria for “sale-leaseback” treatment.

Warranties

The Company generally provides a one-year warranty on instruments. Additionally, the Company provides a warranty on consumables through the expiration date, which generally ranges from six to twelve months after the manufacture date. At the time revenue is recognized, the Company establishes an accrual for estimated warranty expenses based on historical experience as well as anticipated product performance. The Company periodically reviews its warranty reserve for adequacy and adjusts the warranty accrual, if necessary, based on actual experience and estimated costs to be incurred. Warranty expense is recorded as a component of cost of product revenue.

Changes in the Company’s reserve for product warranties during the three and nine months ended October 2, 2016 and September 27, 2015 are as follows (in thousands):



	Three Months Ended						Nine Months Ended
	October 2, 2016			September 27, 2015			October 2, 2016			September 27, 2015
Balance at beginning of period	$	15,679		$	16,365		$	16,717		$	15,616
Additions charged to cost of product revenue	3,878			6,916			17,200			20,737
Repairs and replacements	(5,180		)	(5,348		)	(19,540		)	(18,420		)
Balance at end of period	$	14,377		$	17,933		$	14,377		$	17,933

Leases

Changes in the Company’s facility exit obligation related to its former headquarters lease during the three and nine months ended October 2, 2016 and September 27, 2015 are as follows (in thousands):



	Three Months Ended						Nine Months Ended
	October 2, 2016			September 27, 2015			October 2, 2016			September 27, 2015
Balance at beginning of period	$	20,557		$	36,677		$	22,160		$	37,700
Adjustment to facility exit obligation	66			(5,935		)	87			(5,278		)
Accretion of interest expense	320			590			983			1,926
Cash payments	(1,198		)	(1,539		)	(3,485		)	(4,555		)
Balance at end of period	$	19,745		$	29,793		$	19,745		$	29,793

On March 18, 2016, the Company entered into an agreement to sublease its office building in San Francisco, California. The Company will receive $51.2 million in minimum lease payments during the initial term of approximately eight years.

On April 5, 2016, the Company entered into a lease agreement for certain office buildings being constructed in San Diego, California. Minimum lease payments during the initial term of ten years are estimated to be $127.4 million.

Investments in Consolidated Variable Interest Entities

GRAIL, Inc.

In January 2016, the Company obtained a majority equity ownership interest in GRAIL, Inc. (GRAIL), a company formed with unrelated third party investors to pursue the development and commercialization of a blood test for asymptomatic cancer screening. The Company determined that GRAIL is a variable interest entity as the entity lacks sufficient equity to finance its activities without additional support. Additionally, the Company determined that it has (a) control of the entity’s Board of Directors, which has unilateral power over the activities that most significantly impact the economic performance of GRAIL and (b) the obligation to absorb losses of and the right to receive benefits from GRAIL that are potentially significant to GRAIL. As a result, the Company is deemed to be the primary beneficiary of GRAIL and is required to consolidate GRAIL. On a fully diluted basis, the Company holds a 52% equity ownership interest in GRAIL as of October 2, 2016.

During the three months ended April 3, 2016, GRAIL completed its Series A convertible preferred stock financing, raising $120.0 million, of which the Company invested $40.0 million. Additionally, the Company and GRAIL executed a long-term supply agreement in which the Company contributed certain perpetual licenses, employees, and discounted supply terms in exchange for 112.5 million shares of GRAIL’s Class B Common Stock. Such contributions are recorded at their historical basis as they remain within the control of the Company. The $80.0 million received by GRAIL from unrelated third party investors upon issuance of its Series A convertible preferred stock is classified as noncontrolling interests in stockholders’ equity on the Company’s consolidated balance sheet.

During the three months ended July 3, 2016, GRAIL authorized for issuance 97.5 million shares of Series A-1 convertible preferred stock, all of which were issued to Illumina in exchange for 97.5 million shares of Illumina’s Class B Common Stock on June 23, 2016. As a result of the exchange, Illumina recorded a $9.5 million deemed dividend net of tax of $9.6 million through equity, which was eliminated in consolidation.

For the three months ended October 2, 2016, the Company absorbed approximately 50% of GRAIL’s losses based upon its proportional ownership of GRAIL’s common stock. Prior to the exchange, for the six months ended July 3, 2016, the Company absorbed 90% of GRAIL’s losses based upon its proportional ownership of GRAIL’s common stock.

In accordance with GRAIL’s Equity Incentive Plan, the Company may be required to redeem certain vested stock awards in cash at the then approximate fair market value. The fair value of the redeemable noncontrolling interests is considered a Level 3 instrument. Such redemption right is exercisable at the option of the holder of the awards after February 28, 2021, provided that an initial public offering of GRAIL has not been completed. As the redemption provision is outside of the control of the Company, the redeemable noncontrolling interests in GRAIL are classified outside of stockholders’ equity on the accompanying condensed consolidated balance sheets. The balance of the redeemable noncontrolling interests is reported at the greater of its carrying value after receiving its allocation of GRAIL’s profits and losses or its estimated redemption value at each reporting date.

The assets and liabilities of GRAIL, other than cash and cash equivalents, are not significant to the Company’s financial position as of October 2, 2016. Additionally, GRAIL has an immaterial impact on the Company’s condensed consolidated statements of income and cash flows for the three and nine months ended October 2, 2016.

Helix Holdings I, LLC

In July 2015, the Company obtained a 50% voting equity ownership interest in Helix Holdings I, LLC (Helix), a limited liability company formed with unrelated third party investors to pursue the development and commercialization of a marketplace for consumer genomics. The Company determined that Helix is a variable interest entity as the holder of the at-risk equity investments as a group lack the power to direct the activities of Helix that most significantly impact Helix’s economic performance. Additionally, the Company determined that it has (a) unilateral power over one of the activities that most significantly impacts the economic performance of Helix through its contractual arrangements and no one individual party has unilateral power over the remaining significant activities of Helix and (b) the obligation to absorb losses of and the right to receive benefits from Helix that are potentially significant to Helix. As a result, the Company is deemed to be the primary beneficiary of Helix and is required to consolidate Helix.

As contractually committed, the Company contributed certain perpetual licenses, instruments, intangibles, initial laboratory setup, and discounted supply terms in exchange for voting equity interests in Helix. Such contributions are recorded at their historical basis as they remain within the control of the Company. Helix is financed through cash contributions made by the third party investors in exchange for voting equity interests in Helix.

Certain noncontrolling Helix investors may require the Company to redeem all noncontrolling interests in cash at the then approximate fair market value. The fair value of the redeemable noncontrolling interests is considered a Level 3 instrument. Such redemption right is exercisable at the option of certain noncontrolling interest holders after January 1, 2021, provided that a bona fide pursuit of the sale of Helix has occurred and an initial public offering of Helix has not been completed.

As the contingent redemption is outside of the control of Illumina, the redeemable noncontrolling interests in Helix are classified outside of stockholders’ equity on the accompanying condensed consolidated balance sheets. The balance of the redeemable noncontrolling interests is reported at the greater of its carrying value after receiving its allocation of Helix’s profits and losses or its estimated redemption value at each reporting date. As of October 2, 2016, the noncontrolling shareholders and Illumina each held 50% of Helix’s outstanding voting equity interests.

The assets and liabilities of Helix are not significant to the Company’s financial position as of October 2, 2016. Helix has an immaterial impact on the Company’s condensed consolidated statements of income and cash flows for the three and nine months ended October 2, 2016.

As of October 2, 2016, the accompanying condensed consolidated balance sheet includes $103.6 million of cash and cash equivalents attributable to GRAIL and Helix that will be used to settle their respective obligations and will not be available to settle obligations of the Company.

Redeemable Noncontrolling Interests

The activity of the redeemable noncontrolling interests during the nine months ended October 2, 2016 is as follows (in thousands):



	Redeemable Noncontrolling Interests
Balance as of January 3, 2016	$	32,546
Vesting of redeemable equity awards	1,481
Net loss attributable to noncontrolling interests	(11,793		)
Adjustment up to the redemption value	12,023
Balance as of October 2, 2016	$	34,257

Fair Value Measurements

9 Months Ended

Oct. 02, 2016

Fair Value Disclosures [Abstract]

Fair Value Measurements

The following table presents the Company’s hierarchy for assets and liabilities measured at fair value on a recurring basis as of October 2, 2016 and January 3, 2016 (in thousands):



	October 2, 2016								January 3, 2016
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Assets:
Money market funds (cash equivalents)	$	503,593	$	—	$	—	$	503,593	$	391,246	$	—	$	—	$	391,246
Debt securities in government-sponsored entities	—		29,657		—		29,657		—		14,626		—		14,626
Corporate debt securities	—		463,292		—		463,292		—		421,094		—		421,094
U.S. Treasury securities	248,620		—		—		248,620		181,730		—		—		181,730
Deferred compensation plan assets	—		29,901		—		29,901		—		26,245		—		26,245
Total assets measured at fair value	$	752,213	$	522,850	$	—	$	1,275,063	$	572,976	$	461,965	$	—	$	1,034,941
Liabilities:
Acquisition related contingent consideration liabilities	$	—	$	—	$	5,300	$	5,300	$	—	$	—	$	35,000	$	35,000
Deferred compensation liability	—		28,447		—		28,447		—		24,925		—		24,925
Total liabilities measured at fair value	$	—	$	28,447	$	5,300	$	33,747	$	—	$	24,925	$	35,000	$	59,925

The Company holds available-for-sale securities that consist of highly liquid, investment grade debt securities. The Company considers information provided by the Company’s investment accounting and reporting service provider in the measurement of fair value of its debt securities. The investment service provider provides valuation information from an industry-recognized valuation service. Such valuations may be based on trade prices in active markets for identical assets or liabilities (Level 1 inputs) or valuation models using inputs that are observable either directly or indirectly (Level 2 inputs), such as quoted prices for similar assets or liabilities, yield curve, volatility factors, credit spreads, default rates, loss severity, current market and contractual prices for the underlying instruments or debt, broker and dealer quotes, as well as other relevant economic measures. The Company’s deferred compensation plan assets consist primarily of investments in life insurance contracts carried at cash surrender value, which reflects the net asset value of the underlying publicly traded mutual funds. The Company performs control procedures to corroborate the fair value of its holdings, including comparing valuations obtained from its investment service provider to valuations reported by the Company’s asset custodians, validation of pricing sources and models, and review of key model inputs if necessary.

As a result of an acquisition completed in January 2016, the Company recorded $5.3 million in contingent consideration liabilities, the majority of which are payable within 12 months after the acquisition date. The Company reassesses the fair value of any contingent consideration liabilities on a quarterly basis using the income approach. Assumptions used to estimate the acquisition date fair value of the contingent consideration include discount rates ranging from 4% to 6% and the probability of achieving certain milestones. This fair value measurement of the contingent consideration is based on significant inputs not observed in the market and thus represents a Level 3 measurement. Level 3 instruments are valued based on unobservable inputs that are supported by little or no market activity and reflect the Company’s own assumptions in measuring fair value.

Changes in estimated fair value of contingent consideration liabilities during the nine months ended October 2, 2016 are as follows (in thousands):



	Contingent Consideration Liability (Level 3 Measurement)
Balance as of January 3, 2016	$	35,000
Additional liability recorded as a result of a current period acquisition	5,300
Cash payments	(35,000		)
Balance as of October 2, 2016	$	5,300

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Debt

9 Months Ended

Oct. 02, 2016

Debt Disclosure [Abstract]

Debt

Convertible Senior Notes

As of October 2, 2016, the Company had outstanding $632.5 million in principal amount of 0% convertible senior notes due June 15, 2019 (2019 Notes) and $517.5 million in principal amount of 0.5% convertible senior notes due June 15, 2021 (2021 Notes).

0% Convertible Senior Notes due 2019 and 0.5% Convertible Senior Notes due 2021

In June 2014, the Company issued $632.5 million aggregate principal amount of 2019 Notes and $517.5 million aggregate principal amount of 2021 Notes. The Company used the net proceeds plus cash on hand to repurchase a portion of the outstanding 2016 Notes in privately negotiated transactions concurrently with the issuance of the 2019 and 2021 Notes. The 2019 and 2021 Notes’ mature on June 15, 2019 and June 15, 2021, respectively, and the implied estimated effective rates of the liability components of the Notes were 2.9% and 3.5%, respectively, assuming no conversion.

Both the 2019 and 2021 Notes will be convertible into cash, shares of common stock, or a combination of cash and shares of common stock, at the Company's election, based on an initial conversion rate, subject to adjustment, of 3.9318 shares per $1,000 principal amount of the notes (which represents an initial conversion price of approximately $254.34 per share), only in the following circumstances and to the following extent: (1) during the five business-day period after any 10 consecutive trading day period (the measurement period) in which the trading price per 2019 and 2021 Note for each day of such measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such day; (2) during any calendar quarter (and only during that quarter) after the calendar quarter ending September 30, 2014, if the last reported sale price of the Company’s common stock for 20 or more trading days in the period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter exceeds 130% of the applicable conversion price in effect on the last trading day of the immediately preceding calendar quarter; (3) upon the occurrence of specified events described in the indenture for the 2019 and 2021 Notes; and (4) at any time on or after March 15, 2019 for the 2019 Notes, or March 15, 2021 for the 2021 Notes, through the second scheduled trading day immediately preceding the maturity date.

Neither the 2019 nor the 2021 Notes were convertible as of October 2, 2016 and had no dilutive impact during the three and nine months ended October 2, 2016. If the 2019 and 2021 Notes were converted as of October 2, 2016, the if-converted value would not exceed the principal amount.

0.25% Convertible Senior Notes due 2016

In 2011, the Company issued $920.0 million aggregate principal amount of 0.25% convertible senior notes due 2016 (2016 Notes) with a maturity date of March 15, 2016. The effective rate of the liability component was estimated to be 4.5%. Based upon meeting the stock trading price conversion requirement during the three months ended March 30, 2014, the 2016 Notes became convertible on April 1, 2014 through, and including, March 11, 2016. All notes were converted by March 11, 2016.

During the nine months ended October 2, 2016, the Company recorded a loss on extinguishment of debt calculated as the difference between the estimated fair value of the debt and the carrying value of the notes as of the settlement date. To measure the fair value of the converted notes as of the settlement date, the applicable interest rate was estimated using Level 2 observable inputs and applied to the converted notes using the same methodology as in the issuance date valuation. The loss recorded on extinguishment of debt for the nine months ended October 2, 2016 was immaterial.

The following table summarizes information about the conversion of the 2016 Notes during the nine months ended October 2, 2016 (in thousands):



	2016 Notes
Cash paid for principal of notes converted	$	75,543
Conversion value over principal amount paid in shares of common stock	$	63,753
Number of shares of common stock issued upon conversion	409

Summary of Convertible Senior Notes

The following table summarizes information about the equity and liability components of all convertible senior notes outstanding as of the period reported (dollars in thousands). The fair values of the respective notes outstanding were measured based on quoted market prices, and is a Level 2 measurement.



	October 2, 2016			January 3, 2016
Principal amount of convertible notes outstanding	$	1,150,000		$	1,225,547
Unamortized discount of liability component	(112,716		)	(134,969		)
Net carrying amount of liability component	1,037,284			1,090,578
Less: current portion	—			(74,929		)
Long-term debt	$	1,037,284		$	1,015,649
Carrying value of equity component, net of debt issuance cost	$	161,237		$	213,811
Fair value of outstanding notes	$	1,224,169		$	1,456,451
Weighted-average remaining amortization period of discount on the liability component	3.9 years			4.6 years

Other

As of October 2, 2016, the accompanying condensed consolidated balance sheets include $1.3 million and $3.4 million in current and long-term debt, respectively, related to an outstanding line of credit held by Helix.

Share-based Compensation Expense

9 Months Ended

Oct. 02, 2016

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Share-based Compensation Expense

Share-based compensation expense for all stock awards consists of the following (in thousands):



	Three Months Ended						Nine Months Ended
	October 2, 2016			September 27, 2015			October 2, 2016			September 27, 2015
Cost of product revenue	$	1,799		$	2,567		$	5,949		$	7,012
Cost of service and other revenue	1,261			498			2,114			1,243
Research and development	11,515			9,098			32,889			31,152
Selling, general and administrative	20,008			20,066			60,893			57,697
Share-based compensation expense before taxes	34,583			32,229			101,845			97,104
Related income tax benefits	(7,604		)	(9,876		)	(23,082		)	(28,304		)
Share-based compensation expense, net of taxes	$	26,979		$	22,353		$	78,763		$	68,800

The assumptions used for the specified reporting periods and the resulting estimates of weighted-average fair value per share for stock purchased under the Employee Stock Purchase Plan (ESPP) during the nine months ended October 2, 2016 are as follows:



	Employee Stock Purchase Rights
Risk-free interest rate	0.40% - 0.50%
Expected volatility	40% - 44%
Expected term	0.5 - 1.0 year
Expected dividends	0		%
Weighted-average fair value per share	$	47.88

As of October 2, 2016, approximately $203.2 million of unrecognized compensation cost related to stock options, restricted stock, and ESPP shares granted to date is expected to be recognized over a weighted-average period of approximately 2.4 years.

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

+ References + Details

Stockholders' Equity

9 Months Ended

Oct. 02, 2016

Equity [Abstract]

Stockholders' Equity

Stockholders’ Equity

As of October 2, 2016, approximately 7.5 million shares remained available for future grants under the 2015 Stock Plan and the 2005 Solexa Equity Plan.

Restricted Stock

The Company’s restricted stock activity and related information for the nine months ended October 2, 2016 is as follows (units in thousands):



	Restricted Stock Awards (RSA)	Restricted Stock Units (RSU)		Performance Stock Units (PSU)(1)		Weighted-Average Grant-Date Fair Value per Share
	Restricted Stock Awards (RSA)	Restricted Stock Units (RSU)		Performance Stock Units (PSU)(1)		RSA		RSU		PSU
Outstanding at January 3, 2016	21	2,206		583		$	47.93	$	131.80	$	169.41
Awarded	22	174		30		$	179.00	$	156.32	$	156.75
Vested	—	(383	)	—		$	—	$	85.57	—
Cancelled	—	(197	)	(99	)	$	—	$	136.40	$	163.51
Outstanding at October 2, 2016	43	1,800		514		$	114.59	$	143.46	$	169.81

______________________________________


(1)	The number of units reflect the estimated number of shares to be issued at the end of the performance period.

Stock Options

The Company’s stock option activity under all stock option plans during the nine months ended October 2, 2016 is as follows:



	Options (in thousands)		Weighted-Average Exercise Price
Outstanding at January 3, 2016	1,599		$	41.95
Exercised	(532	)	$	29.65
Cancelled	(2	)	$	46.35
Outstanding at October 2, 2016	1,065		$	48.08

At October 2, 2016, outstanding options to purchase 1.1 million shares were exercisable with a weighted-average exercise price per share of $48.08.

Employee Stock Purchase Plan

The price at which common stock is purchased under the ESPP is equal to 85% of the fair market value of the common stock on the first day of the offering period or purchase date, whichever is lower. During the nine months ended October 2, 2016, approximately 0.2 million shares were issued under the ESPP. As of October 2, 2016, there were approximately 14.3 million shares available for issuance under the ESPP.

Share Repurchases

On July 28, 2016, the Company’s Board of Directors authorized a new share repurchase program, which supersedes all prior and available repurchase authorizations, to repurchase $250.0 million of outstanding common stock. During the three months ended October 2, 2016, 0.1 million shares for $13.1 million were repurchased. During the nine months ended October 2, 2016, the Company repurchased approximately 0.8 million shares for $113.1 million in aggregate. Authorizations to repurchase up to an additional $236.9 million of the Company’s common stock remained available as of October 2, 2016.

Income Taxes	9 Months Ended
Income Taxes	Oct. 02, 2016
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The Company’s effective tax rate may vary from the U.S. federal statutory tax rate due to the change in the mix of earnings in tax jurisdictions with different statutory rates, benefits related to tax credits, and the tax impact of non-deductible expenses and other permanent differences between income before income taxes and taxable income. The effective tax rates for the three and nine months ended October 2, 2016 were 24.2% and 24.9%, respectively. For the three and nine months ended October 2, 2016, the variance from the U.S. federal statutory tax rate of 35% was primarily attributable to the mix of earnings in jurisdictions with lower statutory tax rates than the U.S. federal statutory tax rate, such as in Singapore and the United Kingdom; offset slightly by the tax impact associated with the investments in our consolidated variable interest entities.

Legal Proceedings	9 Months Ended
Legal Proceedings	Oct. 02, 2016
Commitments and Contingencies Disclosure [Abstract]
Legal Proceedings	Legal Proceedings The Company is involved in various lawsuits and claims arising in the ordinary course of business, including actions with respect to intellectual property, employment, and contractual matters. In connection with these matters, the Company assesses, on a regular basis, the probability and range of possible loss based on the developments in these matters. A liability is recorded in the financial statements if it is believed to be probable that a loss has been incurred and the amount of the loss can be reasonably estimated. Because litigation is inherently unpredictable and unfavorable results could occur, assessing contingencies is highly subjective and requires judgments about future events. The Company regularly reviews outstanding legal matters to determine the adequacy of the liabilities accrued and related disclosures. The amount of ultimate loss may differ from these estimates. Each matter presents its own unique circumstances, and prior litigation does not necessarily provide a reliable basis on which to predict the outcome, or range of outcomes, in any individual proceeding. Because of the uncertainties related to the occurrence, amount, and range of loss on any pending litigation or claim, the Company is currently unable to predict their ultimate outcome, and, with respect to any pending litigation or claim where no liability has been accrued, to make a meaningful estimate of the reasonably possible loss or range of loss that could result from an unfavorable outcome. In the event that opposing litigants or claims ultimately succeed at trial and any subsequent appeals on their claims, any potential loss or charges in excess of any established accruals, individually or in the aggregate, could have a material adverse effect on the Company’s business, financial condition, results of operations, and/or cash flows in the period in which the unfavorable outcome occurs or becomes probable, and potentially in future periods. On July 1, 2016, the Company entered into a Settlement and License Agreement with Enzo Life Sciences, Inc. (Enzo) that settled all claims in the litigation. Pursuant to the terms of the Settlement and License Agreement, the Company paid Enzo a one-time payment of $21.0 million for release of past damages claimed and a fully paid-up non-exclusive license to U.S. Patent No. 7,064,197. None of the parties made any admission of liability in entering into the Settlement and License Agreement. The Company allocated the $21.0 million settlement on a relative fair value basis, resulting in $11.5 million capitalized as an intangible asset and a corresponding gain recorded in legal contingencies for the value of the license, which will be amortized over a period of 7 years on a straight-line basis, and the remaining $9.5 million related to past damages claimed. The fair value of the license and past damages was estimated using a discounted cash flow model, and is considered to be a Level 3 measurement.

Segment Information (Notes)

9 Months Ended

Oct. 02, 2016

Segment Reporting [Abstract]

Segment Reporting Disclosure [Text Block]

Segment Information

The Company has two reportable segments: Core Illumina and one segment related to the combined activities of the Company’s consolidated VIEs, GRAIL and Helix. The Company reports segment information based on the management approach. This approach designates the internal reporting used by the Chief Operating Decision Maker (“CODM”) for making decisions and assessing performance as the source of the Company’s reportable segments. The CODM allocates resources and assesses the performance of each operating segment using information about its revenues and income (losses) from operations. Based on the information used by the CODM, the Company has determined its reportable segments as follows:

Core Illumina:

Core Illumina’s products and services serve customers in the research, clinical and applied markets, and enable the adoption of a variety of genomic solutions. Core Illumina includes all operations of the Company, excluding the results of its two consolidated VIEs.

Consolidated VIEs:

GRAIL: GRAIL was created to enable the early detection of cancer in asymptomatic individuals through a simple blood screen based on the concentration of circulating tumor nucleic acids. GRAIL is currently in the early stages of developing this test and as such, has no revenues to date.

Helix: Helix was established to enable individuals to explore their genetic information by providing affordable sequencing and database services for consumers through third party partners, driving the creation of an ecosystem of consumer applications.

Management evaluates the performance of the Company’s operating segments based upon income (loss) from operations. The Company does not allocate expenses between segments. Core Illumina sells products and provides services to GRAIL and Helix in accordance with contractual agreements between the entities.

The following table presents the operating performance of each reportable segment (in thousands):



	Three Months Ended						Nine Months Ended
	October 2, 2016			September 27, 2015			October 2, 2016			September 27, 2015
Segment revenues:
Core Illumina	$	615,135		$	550,271		$	1,792,150		$	1,628,214
Consolidated VIEs	—			—			—			—
Elimination of intersegment revenues	(7,996		)	—			(13,124		)	—
Consolidated revenues	$	607,139		$	550,271		$	1,779,026		$	1,628,214

Segment operating income (loss):
Core Illumina	$	190,742		$	145,893		$	501,411		$	473,952
Consolidated VIEs	(25,136		)	(5,111		)	(49,700		)	(5,111		)
Elimination of intersegment earnings	(4,904		)	—			(7,695		)	—
Consolidated operating income	$	160,702		$	140,782		$	444,016		$	468,841

The following table presents the total assets of each reportable segment (in thousands):



	October 2, 2016			January 3, 2016
Segment assets:
Core Illumina	$	4,095,182		$	3,657,953
Consolidated VIEs	190,904			30,447
Elimination of intersegment assets	(58,259		)	(653		)
Consolidated total assets	$	4,227,827		$	3,687,747

- Definition

The entire disclosure for reporting segments including data and tables. Reportable segments include those that meet any of the following quantitative thresholds a) it's reported revenue, including sales to external customers and intersegment sales or transfers is 10 percent or more of the combined revenue, internal and external, of all operating segments b) the absolute amount of its reported profit or loss is 10 percent or more of the greater, in absolute amount of 1) the combined reported profit of all operating segments that did not report a loss or 2) the combined reported loss of all operating segments that did report a loss c) its assets are 10 percent or more of the combined assets of all operating segments.

+ References

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-Paragraph 31
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8924-108599

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 30
-URI http://asc.fasb.org/extlink&oid=68060357&loc=d3e8906-108599

+ Details

Basis of Presentation and Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Oct. 02, 2016
Accounting Policies [Abstract]
Basis of Presentation	The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (GAAP) for interim financial information and the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements.
Consolidation	The unaudited condensed consolidated financial statements include the accounts of the Company, its wholly-owned subsidiaries, majority-owned or controlled companies, and variable interest entities (VIEs) for which the Company is the primary beneficiary. All intercompany transactions and balances have been eliminated in consolidation. In management’s opinion, the accompanying financial statements reflect all adjustments, consisting of normal recurring adjustments, considered necessary for a fair presentation of the results for the interim periods presented.
Variable Interest Entities	The Company evaluates its ownership, contractual and other interests in entities that are not wholly-owned by the Company to determine if these entities are VIEs, and, if so, whether the Company is the primary beneficiary of the VIE. In determining whether the Company is the primary beneficiary of a VIE and is therefore required to consolidate the VIE, the Company applies a qualitative approach that determines whether it has both (1) the power to direct the activities of the VIE that most significantly impact the VIE’s economic performance and (2) the obligation to absorb losses of, or the rights to receive benefits from, the VIE that could potentially be significant to that VIE. The Company continuously assesses whether it is the primary beneficiary of a VIE as changes to existing relationships or future transactions may result in the consolidation or deconsolidation, as the case may be. The Company has not provided financial or other support during the periods presented to its VIEs that it was not previously contractually required to provide.
Equity Method Investments	The equity method is used to account for investments in which the Company has the ability to exercise significant influence, but not control, over the investee. Such investments are recorded within other assets, and the share of net income or losses of equity investments is recognized on a one quarter lag in other (expense) income, net.
Segment Information	The Company is organized into three operating segments for purposes of evaluating its business operations and reporting its financial results. One operating segment consists of Illumina’s core operations and the other two relate to the Company’s consolidated VIEs. The combined results of operations of the Company’s consolidated VIEs became material for the three and nine months ended October 2, 2016. As such, the Company commenced reporting two segments in the third quarter of 2016. Financial information for all periods presented has been classified to reflect these changes to our reportable segments. For further information on the Company’s segments, refer to note “9. Segment Information”.
Fiscal Year	The Company’s fiscal year consists of 52 or 53 weeks ending the Sunday closest to December 31, with quarters of 13 or 14 weeks ending the Sunday closest to March 31, June 30, September 30, and December 31. The three and nine months ended October 2, 2016 and September 27, 2015 were both 13 and 39 weeks, respectively.
Reclassifications	Certain prior period amounts have been reclassified to conform to the current period presentation.
Recent Accounting Pronouncements	In March 2016, the Financial Accounting Standards Board issued Accounting Standard Update (ASU) 2016-09, Compensation - Stock Compensation (Topic 718). The new standard requires income tax effects of stock compensation awards to be recognized in the income statement when the awards vest or are settled. The new standard also allows the Company to repurchase more of an employee’s shares for tax withholding purposes without triggering liability accounting and to make a policy election to account for forfeitures as they occur. ASU 2016-09 will be effective for the Company beginning in the first quarter of 2017. The Company is currently evaluating the impact of ASU 2016-09 on its consolidated financial statements. In February 2016, the Financial Accounting Standards Board issued ASU 2016-02, Leases (Topic 842). The new standard requires lessees to recognize most leases on their balance sheets as lease liabilities with corresponding right-of-use assets and eliminates certain real estate-specific provisions. ASU 2016-02 will be effective for the Company beginning in the first quarter of 2019. ASU 2016-02 will be adopted on a modified retrospective transition basis for leases existing at, or entered into after, the beginning of the earliest comparative period presented in the financial statements. The Company is currently evaluating the impact of ASU 2016-02 on its consolidated financial statements. In May 2014, the Financial Accounting Standards Board issued ASU 2014-09, Revenue from Contracts with Customers (Topic 606). The new standard is based on the principle that revenue should be recognized to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. ASU 2014-09 will be effective for the Company beginning in the first quarter of 2018 and allows for a full retrospective or a modified retrospective adoption approach. The Company is currently evaluating the impact of ASU 2014-09 on its consolidated financial statements.
Earnings per Share	Basic earnings per share attributable to Illumina stockholders is computed based on the weighted average number of common shares outstanding during the period. Diluted earnings per share attributable to Illumina stockholders is computed based on the sum of the weighted average number of common shares and potentially dilutive common shares outstanding during the period. Per-share earnings of our VIEs are included in the Company’s consolidated basic and diluted earnings per share computations based on the Company’s share of the VIE’s securities. Potentially dilutive common shares consist of shares issuable under convertible senior notes, equity awards, and warrants. Convertible senior notes have a dilutive impact when the average market price of the Company’s common stock exceeds the applicable conversion price of the respective notes. Potentially dilutive common shares from equity awards and warrants are determined using the average share price for each period under the treasury stock method. In addition, the following amounts are assumed to be used to repurchase shares: proceeds from exercise of equity awards and warrants; the average amount of unrecognized compensation expense for equity awards; and estimated tax benefits that will be recorded in additional paid-in capital when expenses related to equity awards become deductible. In loss periods, basic net loss per share and diluted net loss per share are identical because the otherwise dilutive potential common shares become anti-dilutive and are therefore excluded.
Derivatives	The Company is exposed to foreign exchange rate risks in the normal course of business. The Company enters into foreign exchange contracts to manage foreign currency risks related to monetary assets and liabilities that are denominated in currencies other than the U.S. dollar. These foreign exchange contracts are carried at fair value in other assets or other liabilities and are not designated as hedging instruments. Changes in the value of the derivative are recognized in other expense, net, along with the remeasurement gain or loss on the foreign currency denominated assets or liabilities.
Warranties	The Company generally provides a one-year warranty on instruments. Additionally, the Company provides a warranty on consumables through the expiration date, which generally ranges from six to twelve months after the manufacture date. At the time revenue is recognized, the Company establishes an accrual for estimated warranty expenses based on historical experience as well as anticipated product performance. The Company periodically reviews its warranty reserve for adequacy and adjusts the warranty accrual, if necessary, based on actual experience and estimated costs to be incurred. Warranty expense is recorded as a component of cost of product revenue.

Basis of Presentation and Summary of Significant Accounting Policies (Tables)

9 Months Ended

Oct. 02, 2016

Accounting Policies [Abstract]

Summary of Calculation of Weighted Average Shares used to Calculate Basic and Diluted Earnings Per Share, Earnings Per Share

The following table presents the calculation of weighted average shares used to calculate basic and diluted earnings per share (in thousands):



	Three Months Ended		Nine Months Ended
	October 2, 2016	September 27, 2015	October 2, 2016	September 27, 2015
Weighted average shares outstanding	146,705	145,349	146,783	144,447
Effect of potentially dilutive common shares from:
Convertible senior notes	—	1,670	80	2,013
Equity awards	1,196	2,653	1,186	2,648
Weighted average shares used in calculating diluted earnings per share	147,901	149,672	148,049	149,108
Potentially dilutive shares excluded from calculation due to anti-dilutive effect	63	13	580	7

Summary of Calculation of Weighted Average Shares used to Calculate Basic and Diluted Earnings Per Share, Antidilutive Securities

The following table presents the calculation of weighted average shares used to calculate basic and diluted earnings per share (in thousands):



	Three Months Ended		Nine Months Ended
	October 2, 2016	September 27, 2015	October 2, 2016	September 27, 2015
Weighted average shares outstanding	146,705	145,349	146,783	144,447
Effect of potentially dilutive common shares from:
Convertible senior notes	—	1,670	80	2,013
Equity awards	1,196	2,653	1,186	2,648
Weighted average shares used in calculating diluted earnings per share	147,901	149,672	148,049	149,108
Potentially dilutive shares excluded from calculation due to anti-dilutive effect	63	13	580	7

Balance Sheet Account Details (Tables)

9 Months Ended

Oct. 02, 2016

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Summary of Short-term Investments

The following is a summary of short-term investments (in thousands):



	October 2, 2016									January 3, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Available-for-sale securities:
Debt securities in government sponsored entities	$	29,687	$	—	$	(30	)	$	29,657	$	14,634	$	—	$	(8	)	$	14,626
Corporate debt securities	463,484		282		(474		)	463,292		422,177		44		(1,127		)	421,094
U.S. Treasury securities	248,542		182		(104		)	248,620		182,144		3		(417		)	181,730
Total available-for-sale securities	$	741,713	$	464	$	(608	)	$	741,569	$	618,955	$	47	$	(1,552	)	$	617,450

Summary of Contractual Maturities of Available-for-sale Debt Securities

Contractual maturities of available-for-sale debt securities as of October 2, 2016 were as follows (in thousands):



	Estimated Fair Value
Due within one year	$	279,548
After one but within five years	462,021
Total	$	741,569

Summary of Inventory

Inventory consists of the following (in thousands):



	October 2, 2016		January 3, 2016
Raw materials	$	101,646	$	97,740
Work in process	166,050		138,322
Finished goods	44,546		34,715
Total inventory	$	312,242	$	270,777

Summary of Property and Equipment

Property and equipment, net consists of the following (in thousands):



	October 2, 2016			January 3, 2016
Leasehold improvements	$	197,534		$	178,019
Machinery and equipment	264,556			224,158
Computer hardware and software	153,851			136,550
Furniture and fixtures	20,448			18,539
Building	7,670			7,670
Construction in progress	308,825			44,501
Total property and equipment, gross	952,884			609,437
Accumulated depreciation	(319,028		)	(266,743		)
Total property and equipment, net	$	633,856		$	342,694

Summary of Changes in Goodwill

Changes in the Company’s goodwill balance during the nine months ended October 2, 2016 are as follows (in thousands):



	Goodwill
Balance as of January 3, 2016	$	752,629
Current period acquisitions	23,366
Balance as of October 2, 2016	$	775,995

Summary of Accrued Liabilities

Accrued liabilities consist of the following (in thousands):



	October 2, 2016		January 3, 2016
Deferred revenue, current portion	$	116,118	$	96,654
Accrued compensation expenses	89,527		120,662
Accrued taxes payable	30,855		44,159
Customer deposits	17,831		20,901
Acquisition related contingent liability, current portion	7,220		35,000
Other	53,653		69,468
Total accrued liabilities	$	315,204	$	386,844

Summary of Changes in Reserve for Product Warranties

Changes in the Company’s reserve for product warranties during the three and nine months ended October 2, 2016 and September 27, 2015 are as follows (in thousands):



	Three Months Ended						Nine Months Ended
	October 2, 2016			September 27, 2015			October 2, 2016			September 27, 2015
Balance at beginning of period	$	15,679		$	16,365		$	16,717		$	15,616
Additions charged to cost of product revenue	3,878			6,916			17,200			20,737
Repairs and replacements	(5,180		)	(5,348		)	(19,540		)	(18,420		)
Balance at end of period	$	14,377		$	17,933		$	14,377		$	17,933

Summary of Changes in Facility Exit Obligation Related to the Former Headquarters Lease

Changes in the Company’s facility exit obligation related to its former headquarters lease during the three and nine months ended October 2, 2016 and September 27, 2015 are as follows (in thousands):



	Three Months Ended						Nine Months Ended
	October 2, 2016			September 27, 2015			October 2, 2016			September 27, 2015
Balance at beginning of period	$	20,557		$	36,677		$	22,160		$	37,700
Adjustment to facility exit obligation	66			(5,935		)	87			(5,278		)
Accretion of interest expense	320			590			983			1,926
Cash payments	(1,198		)	(1,539		)	(3,485		)	(4,555		)
Balance at end of period	$	19,745		$	29,793		$	19,745		$	29,793

Summary of Activity of Redeemable Noncontrolling Interests

The activity of the redeemable noncontrolling interests during the nine months ended October 2, 2016 is as follows (in thousands):



	Redeemable Noncontrolling Interests
Balance as of January 3, 2016	$	32,546
Vesting of redeemable equity awards	1,481
Net loss attributable to noncontrolling interests	(11,793		)
Adjustment up to the redemption value	12,023
Balance as of October 2, 2016	$	34,257

Fair Value Measurements (Tables)

9 Months Ended

Oct. 02, 2016

Fair Value Disclosures [Abstract]

Summary of Hierarchy for Assets and Liabilities Measured at Fair Value on a Recurring Basis

The following table presents the Company’s hierarchy for assets and liabilities measured at fair value on a recurring basis as of October 2, 2016 and January 3, 2016 (in thousands):



	October 2, 2016								January 3, 2016
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Assets:
Money market funds (cash equivalents)	$	503,593	$	—	$	—	$	503,593	$	391,246	$	—	$	—	$	391,246
Debt securities in government-sponsored entities	—		29,657		—		29,657		—		14,626		—		14,626
Corporate debt securities	—		463,292		—		463,292		—		421,094		—		421,094
U.S. Treasury securities	248,620		—		—		248,620		181,730		—		—		181,730
Deferred compensation plan assets	—		29,901		—		29,901		—		26,245		—		26,245
Total assets measured at fair value	$	752,213	$	522,850	$	—	$	1,275,063	$	572,976	$	461,965	$	—	$	1,034,941
Liabilities:
Acquisition related contingent consideration liabilities	$	—	$	—	$	5,300	$	5,300	$	—	$	—	$	35,000	$	35,000
Deferred compensation liability	—		28,447		—		28,447		—		24,925		—		24,925
Total liabilities measured at fair value	$	—	$	28,447	$	5,300	$	33,747	$	—	$	24,925	$	35,000	$	59,925

Summary of Changes in Estimated Fair Value of Contingent Consideration Liabilities

Changes in estimated fair value of contingent consideration liabilities during the nine months ended October 2, 2016 are as follows (in thousands):



	Contingent Consideration Liability (Level 3 Measurement)
Balance as of January 3, 2016	$	35,000
Additional liability recorded as a result of a current period acquisition	5,300
Cash payments	(35,000		)
Balance as of October 2, 2016	$	5,300

Debt (Tables)

9 Months Ended

Oct. 02, 2016

Debt Disclosure [Abstract]

Summary of Conversion of 2016 Notes

The following table summarizes information about the conversion of the 2016 Notes during the nine months ended October 2, 2016 (in thousands):



	2016 Notes
Cash paid for principal of notes converted	$	75,543
Conversion value over principal amount paid in shares of common stock	$	63,753
Number of shares of common stock issued upon conversion	409

Summary of Information about Equity and Liability Components of Convertible Senior Notes Outstanding

The following table summarizes information about the equity and liability components of all convertible senior notes outstanding as of the period reported (dollars in thousands). The fair values of the respective notes outstanding were measured based on quoted market prices, and is a Level 2 measurement.



	October 2, 2016			January 3, 2016
Principal amount of convertible notes outstanding	$	1,150,000		$	1,225,547
Unamortized discount of liability component	(112,716		)	(134,969		)
Net carrying amount of liability component	1,037,284			1,090,578
Less: current portion	—			(74,929		)
Long-term debt	$	1,037,284		$	1,015,649
Carrying value of equity component, net of debt issuance cost	$	161,237		$	213,811
Fair value of outstanding notes	$	1,224,169		$	1,456,451
Weighted-average remaining amortization period of discount on the liability component	3.9 years			4.6 years

Share-based Compensation Expense (Tables)

9 Months Ended

Oct. 02, 2016

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Summary of Share-based Compensation Expense for all Stock Awards

Share-based compensation expense for all stock awards consists of the following (in thousands):



	Three Months Ended						Nine Months Ended
	October 2, 2016			September 27, 2015			October 2, 2016			September 27, 2015
Cost of product revenue	$	1,799		$	2,567		$	5,949		$	7,012
Cost of service and other revenue	1,261			498			2,114			1,243
Research and development	11,515			9,098			32,889			31,152
Selling, general and administrative	20,008			20,066			60,893			57,697
Share-based compensation expense before taxes	34,583			32,229			101,845			97,104
Related income tax benefits	(7,604		)	(9,876		)	(23,082		)	(28,304		)
Share-based compensation expense, net of taxes	$	26,979		$	22,353		$	78,763		$	68,800

Summary of Assumptions used to Estimate the Weighted-Average Fair Value Per Share for Stock Purchase under the Employee Stock Purchase Plan

The assumptions used for the specified reporting periods and the resulting estimates of weighted-average fair value per share for stock purchased under the Employee Stock Purchase Plan (ESPP) during the nine months ended October 2, 2016 are as follows:



	Employee Stock Purchase Rights
Risk-free interest rate	0.40% - 0.50%
Expected volatility	40% - 44%
Expected term	0.5 - 1.0 year
Expected dividends	0		%
Weighted-average fair value per share	$	47.88

Stockholders' Equity (Tables)

9 Months Ended

Oct. 02, 2016

Equity [Abstract]

Summary of Restricted Stock Activity and Related Information, Restricted Stock

The Company’s restricted stock activity and related information for the nine months ended October 2, 2016 is as follows (units in thousands):



	Restricted Stock Awards (RSA)	Restricted Stock Units (RSU)		Performance Stock Units (PSU)(1)		Weighted-Average Grant-Date Fair Value per Share
	Restricted Stock Awards (RSA)	Restricted Stock Units (RSU)		Performance Stock Units (PSU)(1)		RSA		RSU		PSU
Outstanding at January 3, 2016	21	2,206		583		$	47.93	$	131.80	$	169.41
Awarded	22	174		30		$	179.00	$	156.32	$	156.75
Vested	—	(383	)	—		$	—	$	85.57	—
Cancelled	—	(197	)	(99	)	$	—	$	136.40	$	163.51
Outstanding at October 2, 2016	43	1,800		514		$	114.59	$	143.46	$	169.81

______________________________________


(1)	The number of units reflect the estimated number of shares to be issued at the end of the performance period.

Summary of Restricted Stock Activity and Related Information, Performance Units

The Company’s restricted stock activity and related information for the nine months ended October 2, 2016 is as follows (units in thousands):



	Restricted Stock Awards (RSA)	Restricted Stock Units (RSU)		Performance Stock Units (PSU)(1)		Weighted-Average Grant-Date Fair Value per Share
	Restricted Stock Awards (RSA)	Restricted Stock Units (RSU)		Performance Stock Units (PSU)(1)		RSA		RSU		PSU
Outstanding at January 3, 2016	21	2,206		583		$	47.93	$	131.80	$	169.41
Awarded	22	174		30		$	179.00	$	156.32	$	156.75
Vested	—	(383	)	—		$	—	$	85.57	—
Cancelled	—	(197	)	(99	)	$	—	$	136.40	$	163.51
Outstanding at October 2, 2016	43	1,800		514		$	114.59	$	143.46	$	169.81

______________________________________


(1)	The number of units reflect the estimated number of shares to be issued at the end of the performance period.

Summary of Stock Option Activity Under all Stock Option Plans

The Company’s stock option activity under all stock option plans during the nine months ended October 2, 2016 is as follows:



	Options (in thousands)		Weighted-Average Exercise Price
Outstanding at January 3, 2016	1,599		$	41.95
Exercised	(532	)	$	29.65
Cancelled	(2	)	$	46.35
Outstanding at October 2, 2016	1,065		$	48.08

Segment Information (Tables)

9 Months Ended

Oct. 02, 2016

Segment Reporting [Abstract]

Summary of Operating Performance and Assets by Segment

The following table presents the operating performance of each reportable segment (in thousands):



	Three Months Ended						Nine Months Ended
	October 2, 2016			September 27, 2015			October 2, 2016			September 27, 2015
Segment revenues:
Core Illumina	$	615,135		$	550,271		$	1,792,150		$	1,628,214
Consolidated VIEs	—			—			—			—
Elimination of intersegment revenues	(7,996		)	—			(13,124		)	—
Consolidated revenues	$	607,139		$	550,271		$	1,779,026		$	1,628,214

Segment operating income (loss):
Core Illumina	$	190,742		$	145,893		$	501,411		$	473,952
Consolidated VIEs	(25,136		)	(5,111		)	(49,700		)	(5,111		)
Elimination of intersegment earnings	(4,904		)	—			(7,695		)	—
Consolidated operating income	$	160,702		$	140,782		$	444,016		$	468,841

The following table presents the total assets of each reportable segment (in thousands):



	October 2, 2016			January 3, 2016
Segment assets:
Core Illumina	$	4,095,182		$	3,657,953
Consolidated VIEs	190,904			30,447
Elimination of intersegment assets	(58,259		)	(653		)
Consolidated total assets	$	4,227,827		$	3,687,747

Basis of Presentation and Summary of Significant Accounting Policies - Summary of Calculation of Weighted Average Shares used to Calculate Basic and Diluted Earnings Per Share (Details) - shares shares in Thousands	3 Months Ended		9 Months Ended
	Oct. 02, 2016	Sep. 27, 2015	Oct. 02, 2016	Sep. 27, 2015
Weighted average shares used to calculate basic and diluted earnings per share
Weighted average shares outstanding	146,705	145,349	146,783	144,447
Effect of potentially dilutive common shares from:
Convertible senior notes		1,670	80	2,013
Equity awards	1,196	2,653	1,186	2,648
Weighted average shares used in calculating diluted earnings per share	147,901	149,672	148,049	149,108
Potentially dilutive shares excluded from calculation due to anti-dilutive effect	63	13	580	7

Balance Sheet Account Details - Summary of Short-term Investments (Details) - USD ($) $ in Thousands	Oct. 02, 2016	Jan. 03, 2016
Available-for-sale securities:
Amortized Cost	$ 741,713	$ 618,955
Gross Unrealized Gains	464	47
Gross Unrealized Losses	(608)	(1,552)
Estimated Fair Value	741,569	617,450
Debt securities in government sponsored entities [Member]
Available-for-sale securities:
Amortized Cost	29,687	14,634
Gross Unrealized Losses	(30)	(8)
Estimated Fair Value	29,657	14,626
Corporate debt securities [Member]
Available-for-sale securities:
Amortized Cost	463,484	422,177
Gross Unrealized Gains	282	44
Gross Unrealized Losses	(474)	(1,127)
Estimated Fair Value	463,292	421,094
U.S. Treasury securities [Member]
Available-for-sale securities:
Amortized Cost	248,542	182,144
Gross Unrealized Gains	182	3
Gross Unrealized Losses	(104)	(417)
Estimated Fair Value	$ 248,620	$ 181,730

Balance Sheet Account Details - Summary of Contractual Maturities of Available-for-sale Debt Securities (Details) $ in Thousands	Oct. 02, 2016 USD ($)
Available-for-sale Securities, Debt Maturities, Fair Value, Fiscal Year Maturity [Abstract]
Due within one year	$ 279,548
After one but within five years	462,021
Total	$ 741,569

Balance Sheet Account Details - Narrative - Strategic Investments (Details) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Oct. 02, 2016	Sep. 27, 2015	Oct. 02, 2016	Sep. 27, 2015	Apr. 14, 2016	Jan. 03, 2016
Schedule of Investments [Line Items]
Cost-method investment gain				$ 18.0
Commitment in new venture capital investment fund					$ 100.0
Callable period			10 years
Capital commitment draw down allowed			$ 40.0
Cost-Method Investee [Member]
Schedule of Investments [Line Items]
Revenue from transactions with Company's cost-method investments in non-publicly traded companies	$ 12.5	$ 16.1	42.1	$ 47.3
Other Assets [Member]
Schedule of Investments [Line Items]
Company's cost-method investments in non-publicly traded companies	56.9		56.9			$ 56.6
Equity method investments	3.2		3.2
Cash and Cash Equivalents [Member]
Schedule of Investments [Line Items]
Equity method investments	$ 4.4		$ 4.4

Balance Sheet Account Details - Summary of Inventory (Details) - USD ($) $ in Thousands	Oct. 02, 2016	Jan. 03, 2016
Inventory [Abstract]
Raw materials	$ 101,646	$ 97,740
Work in process	166,050	138,322
Finished goods	44,546	34,715
Total inventory	$ 312,242	$ 270,777

Balance Sheet Account Details - Summary of Property and Equipment (Details) - USD ($) $ in Thousands	Oct. 02, 2016	Jan. 03, 2016
Property, Plant and Equipment [Line Items]
Total property and equipment, gross	$ 952,884	$ 609,437
Accumulated depreciation	319,028	266,743
Total property and equipment, net	633,856	342,694
Leasehold improvements
Property, Plant and Equipment [Line Items]
Total property and equipment, gross	197,534	178,019
Machinery and equipment
Property, Plant and Equipment [Line Items]
Total property and equipment, gross	264,556	224,158
Computer hardware and software
Property, Plant and Equipment [Line Items]
Total property and equipment, gross	153,851	136,550
Furniture and fixtures
Property, Plant and Equipment [Line Items]
Total property and equipment, gross	20,448	18,539
Building
Property, Plant and Equipment [Line Items]
Total property and equipment, gross	7,670	7,670
Construction in progress
Property, Plant and Equipment [Line Items]
Total property and equipment, gross	$ 308,825	$ 44,501

Balance Sheet Account Details - Narrative - Property and Equipment (Details) $ in Millions	9 Months Ended
	Oct. 02, 2016 USD ($)
Property, Plant and Equipment [Line Items]
Accrued expenditures included in capital expenditures	$ 194.4
Construction in progress
Property, Plant and Equipment [Line Items]
Accrued expenditures included in capital expenditures	$ 168.8

Balance Sheet Account Details - Summary of Changes in Goodwill (Details) $ in Thousands	9 Months Ended
	Oct. 02, 2016 USD ($)
Goodwill [Roll Forward]
Beginning balance	$ 752,629
Current period acquisitions	23,366
Ending balance	$ 775,995

Balance Sheet Account Details - Narrative - Goodwill (Details) $ in Millions	1 Months Ended
	Jan. 31, 2016 USD ($) business
Goodwill and Intangible Assets Disclosure [Abstract]
Number of acquisitions closed \| business	2
Upfront cash payments, equity instruments and certain contingent consideration provisions \| $	$ 17.8

Balance Sheet Account Details - Narrative - Derivatives (Details) - USD ($) $ in Millions	Oct. 02, 2016	Jan. 03, 2016
Not Designated as Hedging Instrument [Member] \| Foreign Exchange Forward [Member]
Derivative [Line Items]
Derivative, notional amount	$ 62.2	$ 61.3

Balance Sheet Account Details - Summary of Accrued Liabilities (Details) - USD ($) $ in Thousands	Oct. 02, 2016	Jan. 03, 2016
Accrued Liabilities, Current [Abstract]
Deferred revenue, current portion	$ 116,118	$ 96,654
Accrued compensation expenses	89,527	120,662
Accrued taxes payable	30,855	44,159
Customer deposits	17,831	20,901
Acquisition related contingent liability, current portion	7,220	35,000
Other	53,653	69,468
Total accrued liabilities	$ 315,204	$ 386,844

- Definition

The carrying amount of consideration received or receivable as of the balance sheet date on potential earnings that were not recognized as revenue in conformity with GAAP, and which are expected to be recognized as such within one year or the normal operating cycle, if longer, including sales, license fees, and royalties, but excluding interest income.

+ References + Details

Balance Sheet Account Details - Narrative - Build-to-Suit Lease Liability (Details) $ in Thousands	Oct. 02, 2016 USD ($) Leases	Jan. 03, 2016 USD ($)
Leases [Abstract]
Number of projects accounted for under build-to-suit lease accounting \| Leases	3
Build-to-suit lease liability \| $	$ 178,311	$ 9,495

Balance Sheet Account Details - Narrative - Warranties (Details)	9 Months Ended
	Oct. 02, 2016
Instruments [Member]
Product Warranty Liability [Line Items]
Warranty period	1 year
Consumables [Member] \| Minimum [Member]
Product Warranty Liability [Line Items]
Warranty period	6 months
Consumables [Member] \| Maximum [Member]
Product Warranty Liability [Line Items]
Warranty period	12 months

Balance Sheet Account Details - Summary of Changes in Reserve for Product Warranties (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Oct. 02, 2016	Sep. 27, 2015	Oct. 02, 2016	Sep. 27, 2015
Reserve for product warranties [Roll Forward]
Balance at beginning of period	$ 15,679	$ 16,365	$ 16,717	$ 15,616
Additions charged to cost of product revenue	3,878	6,916	17,200	20,737
Repairs and replacements	(5,180)	(5,348)	(19,540)	(18,420)
Balance at end of period	$ 14,377	$ 17,933	$ 14,377	$ 17,933

Balance Sheet Account Details - Summary of Changes in Facility Exit Obligation Related to the Former Headquarters Lease (Details) - Facility Exit Obligation [Member] - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Oct. 02, 2016	Sep. 27, 2015	Oct. 02, 2016	Sep. 27, 2015
Headquarter Facility Exit Obligation [Roll Forward]
Balance at beginning of period	$ 20,557	$ 36,677	$ 22,160	$ 37,700
Adjustment to facility exit obligation	66	(5,935)	87	(5,278)
Accretion of interest expense	320	590	983	1,926
Cash payments	(1,198)	(1,539)	(3,485)	(4,555)
Balance at end of period	$ 19,745	$ 29,793	$ 19,745	$ 29,793

Balance Sheet Account Details - Narrative - Leases (Details) - USD ($) $ in Millions	Apr. 05, 2016	Mar. 18, 2016
March 2016 Lease Agreements [Member]
Capital Leased Assets [Line Items]
Future minimum payments to be received under sublease		$ 51.2
Operating lease term		8 years
April 2016 Lease Agreements [Member]
Capital Leased Assets [Line Items]
Capital lease term	10 years
Future minimum payment due for lease addition in period	$ 127.4

Balance Sheet Account Details - Narrative - Investment in Consolidated Variable Interest Entities (Details) - USD ($) $ in Thousands, shares in Millions	3 Months Ended		6 Months Ended	9 Months Ended
	Jul. 03, 2016	Apr. 03, 2016	Jul. 03, 2016	Oct. 02, 2016	Sep. 27, 2015	Jan. 03, 2016	Jul. 31, 2015	Dec. 28, 2014
Variable Interest Entity [Line Items]
Contributions from noncontrolling interest owners				$ 80,000	$ 32,128
Noncontrolling shareholders interest percentage				50.00%
Cash and cash equivalents attributable to variable interest entities				$ 794,697	$ 551,529	$ 768,770		$ 636,154
Variable Interest Entity, Primary Beneficiary [Member]
Variable Interest Entity [Line Items]
Cash and cash equivalents attributable to variable interest entities				$ 103,600
GRAIL, Inc. [Member]
Variable Interest Entity [Line Items]
Deemed dividend	$ 9,500
Deemed dividend, tax effect	$ 9,600
GRAIL, Inc. [Member] \| Variable Interest Entity, Primary Beneficiary [Member]
Variable Interest Entity [Line Items]
Equity ownership interest percentage				52.00%
Series A financing		$ 120,000
Amount contributed		40,000
Contributions from noncontrolling interest owners		$ 80,000
Percentage of entity's losses absorbed			90.00%
Helix Holdings I, LLC [Member] \| Variable Interest Entity, Primary Beneficiary [Member]
Variable Interest Entity [Line Items]
Equity ownership interest percentage				50.00%			50.00%
GRAIL Class B [Member] \| GRAIL, Inc. [Member] \| Variable Interest Entity, Primary Beneficiary [Member]
Variable Interest Entity [Line Items]
Stock exchanged (in shares)		112.5
GRAIL Class A-1 Convertible [Member] \| GRAIL, Inc. [Member] \| Variable Interest Entity, Primary Beneficiary [Member]
Variable Interest Entity [Line Items]
Stock exchanged (in shares)	97.5
Illumina Class B [Member] \| GRAIL, Inc. [Member] \| Variable Interest Entity, Primary Beneficiary [Member]
Variable Interest Entity [Line Items]
Stock exchanged (in shares)	97.5

Balance Sheet Account Details - Summary of Activity of Redeemable Noncontrolling Interests (Details) $ in Thousands	9 Months Ended
	Oct. 02, 2016 USD ($)
Increase (Decrease) in Redeemable Noncontrolling Interests [Roll Forward]
Balance as of January 3, 2016	$ 32,546
Vesting of redeemable equity awards	1,481
Net loss attributable to noncontrolling interests	(11,793)
Adjustment up to the redemption value	12,023
Balance as of October 2, 2016	$ 34,257

Fair Value Measurements - Summary of Hierarchy for Assets and Liabilities Measured at Fair Value on a Recurring Basis (Details) - USD ($) $ in Thousands	Oct. 02, 2016	Jan. 03, 2016
Assets:
Available-for-sale securities	$ 741,569	$ 617,450
Debt securities in government sponsored entities [Member]
Assets:
Available-for-sale securities	29,657	14,626
Corporate debt securities [Member]
Assets:
Available-for-sale securities	463,292	421,094
U.S. Treasury securities [Member]
Assets:
Available-for-sale securities	248,620	181,730
Fair Value, Measurements, Recurring [Member]
Assets:
Deferred compensation plan assets	29,901	26,245
Total assets measured at fair value	1,275,063	1,034,941
Liabilities:
Acquisition related contingent consideration liabilities	5,300	35,000
Deferred compensation liability	28,447	24,925
Total liabilities measured at fair value	33,747	59,925
Fair Value, Measurements, Recurring [Member] \| Debt securities in government sponsored entities [Member]
Assets:
Available-for-sale securities	29,657	14,626
Fair Value, Measurements, Recurring [Member] \| Corporate debt securities [Member]
Assets:
Available-for-sale securities	463,292	421,094
Fair Value, Measurements, Recurring [Member] \| U.S. Treasury securities [Member]
Assets:
Available-for-sale securities	248,620	181,730
Fair Value, Measurements, Recurring [Member] \| Money market funds (cash equivalents) [Member]
Assets:
Money market funds (cash equivalents)	503,593	391,246
Fair Value, Measurements, Recurring [Member] \| Level 1 [Member]
Assets:
Total assets measured at fair value	752,213	572,976
Fair Value, Measurements, Recurring [Member] \| Level 1 [Member] \| U.S. Treasury securities [Member]
Assets:
Available-for-sale securities	248,620	181,730
Fair Value, Measurements, Recurring [Member] \| Level 1 [Member] \| Money market funds (cash equivalents) [Member]
Assets:
Money market funds (cash equivalents)	503,593	391,246
Fair Value, Measurements, Recurring [Member] \| Level 2 [Member]
Assets:
Deferred compensation plan assets	29,901	26,245
Total assets measured at fair value	522,850	461,965
Liabilities:
Deferred compensation liability	28,447	24,925
Total liabilities measured at fair value	28,447	24,925
Fair Value, Measurements, Recurring [Member] \| Level 2 [Member] \| Debt securities in government sponsored entities [Member]
Assets:
Available-for-sale securities	29,657	14,626
Fair Value, Measurements, Recurring [Member] \| Level 2 [Member] \| Corporate debt securities [Member]
Assets:
Available-for-sale securities	463,292	421,094
Fair Value, Measurements, Recurring [Member] \| Level 3 [Member]
Liabilities:
Acquisition related contingent consideration liabilities	5,300	35,000
Total liabilities measured at fair value	$ 5,300	$ 35,000

Fair Value Measurements - Narrative (Details) - Contingent Consideration Liability [Member] $ in Thousands	9 Months Ended
	Oct. 02, 2016 USD ($)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Additional liability recorded as a result of a current period acquisition	$ 5,300
Fair Value, Measurements, Recurring [Member] \| Level 3 [Member] \| Minimum [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Discount rate for assessment of the acquisition date fair value	4.00%
Fair Value, Measurements, Recurring [Member] \| Level 3 [Member] \| Maximum [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Discount rate for assessment of the acquisition date fair value	6.00%

Fair Value Measurements - Summary of Changes in Estimated Fair Value of Contingent Consideration Liabilities (Details) - Contingent Consideration Liability [Member] $ in Thousands	9 Months Ended
	Oct. 02, 2016 USD ($)
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Beginning balance	$ 35,000
Additional liability recorded as a result of a current period acquisition	5,300
Cash payments	(35,000)
Ending balance	$ 5,300

Debt - Narrative (Details) - Convertible Senior Notes [Member]	1 Months Ended	9 Months Ended
	Jun. 29, 2014 USD ($) $ / shares	Oct. 02, 2016 USD ($) day	Dec. 31, 2011 USD ($)
2019 Notes [Member]
Debt Instrument [Line Items]
Principal amount \| $	$ 632,500,000	$ 632,500,000
Interest rate on convertible senior notes		0.00%
Effective interest rate used to measure fair value of converted notes upon conversion	2.90%
Conversion rate	0.0039318
Conversion price (in dollars per share) \| $ / shares	$ 254.34
Threshold note trading days		5
Threshold consecutive note trading days		10 days
Threshold percentage of note price trigger		98.00%
Threshold common stock trading days		20
Threshold consecutive common stock trading days		30 days
Threshold percentage of common stock price trigger		130.00%
2021 Notes [Member]
Debt Instrument [Line Items]
Principal amount \| $	$ 517,500,000	$ 517,500,000
Interest rate on convertible senior notes		0.50%
Effective interest rate used to measure fair value of converted notes upon conversion	3.50%
Conversion rate	0.0039318
Conversion price (in dollars per share) \| $ / shares	$ 254.34
Threshold note trading days		5
Threshold consecutive note trading days		10 days
Threshold percentage of note price trigger		98.00%
Threshold common stock trading days		20
Threshold consecutive common stock trading days		30 days
Threshold percentage of common stock price trigger		130.00%
2016 Notes [Member]
Debt Instrument [Line Items]
Principal amount \| $			$ 920,000,000
Interest rate on convertible senior notes			0.25%
Effective interest rate used to measure fair value of converted notes upon conversion			4.50%

Debt - Summary of Conversion of 2016 Notes (Details) - Convertible Senior Notes [Member] - 2016 Notes [Member] shares in Thousands, $ in Thousands	9 Months Ended
	Oct. 02, 2016 USD ($) shares
Extinguishment of Debt [Line Items]
Cash paid for principal of notes converted	$ 75,543
Conversion value over principal amount paid in shares of common stock	$ 63,753
Number of shares of common stock issued upon conversion \| shares	409

Debt - Summary of Information about Equity and Liability Components of Convertible Senior Notes Outstanding (Details) - USD ($) $ in Thousands	9 Months Ended	12 Months Ended
	Oct. 02, 2016	Jan. 03, 2016
Summarized information about equity and liability components of convertible senior notes
Less: current portion	$ (1,250)	$ (74,929)
Long-term debt	1,040,765	1,015,649
Convertible Senior Notes [Member]
Summarized information about equity and liability components of convertible senior notes
Principal amount of convertible notes outstanding	1,150,000	1,225,547
Unamortized discount of liability component	(112,716)	(134,969)
Net carrying amount of liability component	1,037,284	1,090,578
Less: current portion		(74,929)
Long-term debt	1,037,284	1,015,649
Carrying value of equity component, net of debt issuance cost	$ 161,237	$ 213,811
Weighted-average remaining amortization period of discount on the liability component	3 years 11 months	4 years 7 months
Fair Value, Inputs, Level 2 [Member] \| Convertible Senior Notes [Member]
Summarized information about equity and liability components of convertible senior notes
Fair value of outstanding notes	$ 1,224,169	$ 1,456,451

Debt - Other Narrative (Details) - USD ($) $ in Thousands	Oct. 02, 2016	Jan. 03, 2016
Line of Credit Facility [Line Items]
Long-term debt, current portion	$ 1,250	$ 74,929
Long-term debt	1,040,765	$ 1,015,649
Helix Holdings I, LLC [Member] \| Line of Credit [Member]
Line of Credit Facility [Line Items]
Long-term debt, current portion	1,300
Long-term debt	$ 3,400

Share-based Compensation Expense - Summary of Share-based Compensation Expense for all Stock Awards (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Oct. 02, 2016	Sep. 27, 2015	Oct. 02, 2016	Sep. 27, 2015
Share-based Compensation
Share-based compensation expense before taxes	$ 34,583	$ 32,229	$ 101,845	$ 97,104
Related income tax benefits	(7,604)	(9,876)	(23,082)	(28,304)
Share-based compensation expense, net of taxes	26,979	22,353	78,763	68,800
Cost of product revenue [Member]
Share-based Compensation
Share-based compensation expense before taxes	1,799	2,567	5,949	7,012
Cost of service and other revenue [Member]
Share-based Compensation
Share-based compensation expense before taxes	1,261	498	2,114	1,243
Research and development [Member]
Share-based Compensation
Share-based compensation expense before taxes	11,515	9,098	32,889	31,152
Selling, general and administrative [Member]
Share-based Compensation
Share-based compensation expense before taxes	$ 20,008	$ 20,066	$ 60,893	$ 57,697

Share-based Compensation Expense - Summary of Assumptions used to Estimate the Weighted-Average Fair Value Per Share for Stock Purchase under the Employee Stock Purchase Plan (Details) - Employee Stock [Member]	9 Months Ended
	Oct. 02, 2016 $ / shares
Assumptions used to estimate the fair value per share of employee stock purchase rights granted
Expected volatility, minimum	40.00%
Expected volatility, maximum	44.00%
Expected dividends	0.00%
Weighted-average fair value per share (in dollars per share)	$ 47.88
Minimum [Member]
Assumptions used to estimate the fair value per share of employee stock purchase rights granted
Risk-free interest rate	0.40%
Expected term	6 months
Maximum [Member]
Assumptions used to estimate the fair value per share of employee stock purchase rights granted
Risk-free interest rate	0.50%
Expected term	1 year

Share-based Compensation Expense - Narrative (Details) $ in Millions	9 Months Ended
	Oct. 02, 2016 USD ($)
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Unrecognized compensation cost related to stock options, restricted stock, and ESPP shares granted to date	$ 203.2
Weighted-average period of unrecognized compensation cost related to stock options, restricted stock, and ESPP shares granted to date	2 years 5 months

Stockholders' Equity - Narrative (Details) shares in Millions	Oct. 02, 2016 shares
2015 Illumina and 2005 Solexa Plans [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for issuance (in shares)	7.5

Stockholders' Equity - Summary of Restricted Stock Activity and Related Information (Details) shares in Thousands	9 Months Ended
	Oct. 02, 2016 $ / shares shares
Restricted Stock Awards (RSA) [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Outstanding at period start (in shares) \| shares	21
Awarded (in shares) \| shares	22
Outstanding at period end (in shares) \| shares	43
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Weighted-Average Grant Date Fair Value per Share, Outstanding at period start (in dollars per share) \| $ / shares	$ 47.93
Weighted-Average Grant Date Fair Value per Share, Awarded (in dollars per share) \| $ / shares	179.00
Weighted-Average Grant Date Fair Value per Share, Outstanding at period end (in dollars per share) \| $ / shares	$ 114.59
Restricted Stock Units (RSU) [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Outstanding at period start (in shares) \| shares	2,206
Awarded (in shares) \| shares	174
Vested (in shares) \| shares	(383)
Cancelled (in shares) \| shares	(197)
Outstanding at period end (in shares) \| shares	1,800
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Weighted-Average Grant Date Fair Value per Share, Outstanding at period start (in dollars per share) \| $ / shares	$ 131.80
Weighted-Average Grant Date Fair Value per Share, Awarded (in dollars per share) \| $ / shares	156.32
Weighted-Average Grant Date Fair Value per Share, Vested (in dollars per share) \| $ / shares	85.57
Weighted-Average Grant Date Fair Value per Share, Cancelled (in dollars per share) \| $ / shares	136.40
Weighted-Average Grant Date Fair Value per Share, Outstanding at period end (in dollars per share) \| $ / shares	$ 143.46
Performance Stock Units (PSU) [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Outstanding at period start (in shares) \| shares	583
Awarded (in shares) \| shares	30
Cancelled (in shares) \| shares	(99)
Outstanding at period end (in shares) \| shares	514
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Weighted-Average Grant Date Fair Value per Share, Outstanding at period start (in dollars per share) \| $ / shares	$ 169.41
Weighted-Average Grant Date Fair Value per Share, Awarded (in dollars per share) \| $ / shares	156.75
Weighted-Average Grant Date Fair Value per Share, Cancelled (in dollars per share) \| $ / shares	163.51
Weighted-Average Grant Date Fair Value per Share, Outstanding at period end (in dollars per share) \| $ / shares	$ 169.81

Stockholders' Equity - Summary of Stock Option Activity Under all Stock Option Plans (Details) shares in Thousands	9 Months Ended
	Oct. 02, 2016 $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Options, Outstanding at period start (in shares) \| shares	1,599
Options, Exercised (in shares) \| shares	(532)
Options, Cancelled (in shares) \| shares	(2)
Options, Outstanding at period end (in shares) \| shares	1,065
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price [Abstract]
Weighted-Average Exercise Price, Options, Outstanding at period start (in dollars per share) \| $ / shares	$ 41.95
Weighted-Average Exercise Price, Options, Exercised (in dollars per share) \| $ / shares	29.65
Weighted-Average Exercise Price, Options, Cancelled (in dollars per share) \| $ / shares	46.35
Weighted-Average Exercise Price, Options, Outstanding at period end (in dollars per share) \| $ / shares	$ 48.08

Stockholders' Equity - Narrative - Stock Options (Details) shares in Millions	Oct. 02, 2016 $ / shares shares
Equity [Abstract]
Stock options exercisable (in shares) \| shares	1.1
Stock options exercisable outstanding weighted-average exercise price per share (in dollars per share) \| $ / shares	$ 48.08

Stockholders' Equity - Narrative - Employee Stock Purchase Plan (Details) - ESPP [Member] - Employee Stock [Member] shares in Millions	9 Months Ended
	Oct. 02, 2016 shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Specified percentage of the fair market value of the common stock on the first or last day of the offering period whichever is lower at which stock is purchased	85.00%
Total shares issued under the ESPP (in shares)	0.2
Shares available for issuance (in shares)	14.3

Stockholders' Equity - Narrative - Share Repurchases (Details) - USD ($) $ in Thousands, shares in Millions	3 Months Ended	9 Months Ended
	Oct. 02, 2016	Oct. 02, 2016	Sep. 27, 2015	Jul. 28, 2016
Class of Stock [Line Items]
Common stock repurchases		$ 113,075	$ 72,256
Common Stock [Member]
Class of Stock [Line Items]
Repurchase of common shares (in shares)	0.1	0.8
Common stock repurchases	$ 13,100	$ 113,100
Additional amount authorized to repurchase	$ 236,900	$ 236,900
Common Stock [Member] \| July 2016 Share Repurchase Plan [Member]
Class of Stock [Line Items]
Stock repurchase program, authorized amount				$ 250,000

Income Taxes - Narrative (Details)	3 Months Ended	9 Months Ended
Income Taxes - Narrative (Details)	Oct. 02, 2016	Oct. 02, 2016
Income Tax Disclosure [Abstract]
Effective tax rate	24.20%	24.90%
U.S. federal statutory tax rate	35.00%	35.00%

Legal Proceedings - Narrative (Details) - Settled Litigation [Member] - Enzo [Member] $ in Millions	9 Months Ended
	Oct. 02, 2016 USD ($)
Loss Contingencies [Line Items]
Settlement payment	$ 21.0
Amortization period of intangible asset	7 years
Finite-Lived Intangible Assets [Member]
Loss Contingencies [Line Items]
Settlement payment	$ 11.5
Release Of Past Damages [Member]
Loss Contingencies [Line Items]
Settlement payment	$ 9.5

Segment Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Segment Information (Details) - USD ($) $ in Thousands	Oct. 02, 2016	Sep. 27, 2015	Oct. 02, 2016	Sep. 27, 2015	Jan. 03, 2016
Segment Reporting Information [Line Items]
Segment revenues	$ 607,139	$ 550,271	$ 1,779,026	$ 1,628,214
Segment operating income (loss)	160,702	140,782	444,016	468,841
Segment assets	4,227,827		4,227,827		$ 3,687,747
Core Illumina
Segment Reporting Information [Line Items]
Segment revenues	615,135	550,271	1,792,150	1,628,214
Segment operating income (loss)	190,742	145,893	501,411	473,952
Segment assets	4,095,182		4,095,182		3,657,953
Consolidated VIEs
Segment Reporting Information [Line Items]
Segment operating income (loss)	(25,136)	$ (5,111)	(49,700)	$ (5,111)
Segment assets	190,904		190,904		30,447
Intersegment Eliminations
Segment Reporting Information [Line Items]
Segment revenues	(7,996)		(13,124)
Segment operating income (loss)	(4,904)		(7,695)
Segment assets	$ (58,259)		$ (58,259)		$ (653)