Illumina (ILMN) 10-Q 7 May 14 2014 Q1 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	3 Months Ended
In Millions, unless otherwise specified	Mar. 30, 2014	Apr. 11, 2014
Document and Entity Information [Abstract]	'	'
Entity Registrant Name	'Illumina Inc	'
Entity Central Index Key	'0001110803	'
Document Type	'10-Q	'
Document Period End Date	30-Mar-14	'
Amendment Flag	'false	'
Document Fiscal Year Focus	'2014	'
Document Fiscal Period Focus	'Q1	'
Current Fiscal Year End Date	'--12-28	'
Entity Filer Category	'Large Accelerated Filer	'
Entity Common Stock, Shares Outstanding	'	128.4

Condensed_Consolidated_Balance

Condensed Consolidated Balance Sheets (Unaudited) (USD $)	Mar. 30, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$518,513	$711,637
Short-term investments	573,289	453,966
Accounts receivable, net	293,045	238,946
Inventory	164,231	154,099
Deferred tax assets, current portion	40,349	36,076
Prepaid expenses and other current assets	42,516	22,811
Total current assets	1,631,943	1,617,535
Property and equipment, net	210,372	202,666
Goodwill	723,259	723,061
Intangible assets, net	316,984	331,173
Deferred tax assets, long-term portion	101,336	88,480
Other assets	69,676	56,091
Total assets	3,053,570	3,019,006
Current liabilities:	'	'
Accounts payable	86,471	73,655
Accrued liabilities	215,292	219,120
Long-term debt, current portion	848,016	29,288
Total current liabilities	1,149,779	322,063
Long-term debt	0	839,305
Long-term legal contingencies	138,780	132,933
Other long-term liabilities	191,398	191,221
Conversion option subject to cash settlement	'	282
Stockholders' equity:	'	'
Preferred stock	0	0
Common stock	1,778	1,753
Additional paid-in capital	2,681,983	2,562,705
Accumulated other comprehensive income	1,208	1,234
Retained earnings	267,832	207,855
Treasury stock, at cost	-1,379,188	-1,240,345
Total stockholders’ equity	1,573,613	1,533,202
Total liabilities and stockholders’ equity	$3,053,570	$3,019,006

Condensed_Consolidated_Stateme

Condensed Consolidated Statements of Operations (Unaudited) (USD $)	3 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Mar. 30, 2014	Mar. 31, 2013
Revenue:	'	'
Product revenue	$362,211	$296,170
Service and other revenue	58,570	34,788
Total revenue	420,781	330,958
Cost of revenue:	'	'
Cost of product revenue	111,441	89,978
Cost of service and other revenue	21,513	15,138
Amortization of acquired intangible assets	9,535	6,550
Total cost of revenue	142,489	111,666
Gross profit	278,292	219,292
Operating expense:	'	'
Research and development	77,041	61,450
Selling, general and administrative	109,573	85,074
Acquisition related (gain) expense, net	-1,013	3,821
Headquarter relocation	595	757
Legal contingencies	'	105,853
Unsolicited tender offer related expense	'	7,484
Total operating expense	186,196	264,439
Income (loss) from operations	92,096	-45,147
Other income (expense):	'	'
Interest income	956	1,933
Interest expense	-9,743	-9,747
Cost-method investment related gain	'	6,113
Other income (expense), net	479	-714
Total other expense, net	-8,308	-2,415
Income (loss) before income taxes	83,788	-47,562
Provision for (benefit from) income taxes	23,811	-24,975
Net income (loss)	$59,977	($22,587)
Net income (loss) per basic share	$0.47	($0.18)
Net income (loss) per diluted share	$0.40	($0.18)
Shares used in calculating basic net income (loss) per share	128,146	123,768
Shares used in calculating diluted net income (loss) per share	150,619	123,768

Condensed_Consolidated_Stateme1

Condensed Consolidated Statements of Comprehensive Income (Loss) (Unaudited) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Mar. 30, 2014	Mar. 31, 2013
Statement of Comprehensive Income [Abstract]	'	'
Net income (loss)	$59,977	($22,587)
Unrealized loss on available-for-sale securities, net of deferred tax	-26	-420
Total comprehensive income (loss)	$59,951	($23,007)

Condensed_Consolidated_Stateme2

Condensed Consolidated Statements of Cash Flows (Unaudited) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Mar. 30, 2014	Mar. 31, 2013
Cash flows from operating activities:	'	'
Net Income (Loss)	$59,977	($22,587)
Adjustments to reconcile net income (loss) to net cash provided by operating activities:	'	'
Depreciation expense	14,593	11,759
Amortization of intangible assets	13,814	8,772
Share-based compensation expense	33,424	24,219
Accretion of debt discount	8,992	9,009
Contingent compensation expense	2,417	1,393
Incremental tax benefit related to share-based compensation	-50,528	-5,278
Deferred income taxes	33,943	-36,704
Change in fair value of contingent consideration	-1,760	464
Cost-method investment related gain	'	-6,113
Other	-636	4,107
Changes in operating assets and liabilities:	'	'
Accounts receivable	-52,156	6,129
Inventory	-9,991	-8,266
Prepaid expenses and other current assets	125	1,536
Other assets	-8,972	-2,088
Accounts payable	10,060	8,459
Accrued liabilities	-23,147	-15,267
Accrued legal contingencies	5,847	106,922
Other long-term liabilities	1,085	1,374
Net cash provided by operating activities	37,087	87,840
Cash flows from investing activities:	'	'
Purchases of available-for-sale securities	-253,255	-97,480
Sales of available-for-sale securities	89,030	278,181
Maturities of available-for-sale securities	44,075	111,333
Net cash paid for acquisitions	'	-345,111
(Purchases of) sales proceeds from strategic investments	-4,600	9,998
Purchases of property and equipment	-19,012	-21,441
Cash paid for intangible assets	-625	-501
Net cash used in investing activities	-144,387	-65,021
Cash flows from financing activities:	'	'
Payments on financing obligations	-29,654	-58
Payments on acquisition related contingent consideration liability	'	-3,985
Incremental tax benefit related to share-based compensation	50,528	5,278
Common stock repurchases	-130,017	-25,011
Taxes paid related to net share settlement of equity awards	-8,826	-2,468
Proceeds from issuance of common stock	32,045	13,238
Net cash used in financing activities	-85,924	-13,006
Effect of exchange rate changes on cash and cash equivalents	100	-712
Net (decrease) increase in cash and cash equivalents	-193,124	9,101
Cash and cash equivalents at beginning of period	711,637	433,981
Cash and cash equivalents at end of period	$518,513	$443,082

Summary_of_Significant_Account

Summary of Significant Accounting Policies	3 Months Ended
	Mar. 30, 2014
Accounting Policies [Abstract]	'
Summary of Significant Accounting Policies	'
	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. The unaudited condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries. 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.
	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 December 29, 2013, 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.
	Segment Information
	Effective December 30, 2013, the Company reorganized and separated the roles of the Chief Executive Officer and the President, with core market and operational functions centralized and reporting to the President for the primary purpose of achieving scalability in business operations to support the growth in its strategic markets. Corporate functions and the President report to the CEO. As a result, the Company operates under one operating segment and reports under one reportable segment.
	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 months ended March 30, 2014 and March 31, 2013 were both 13 weeks.
	Derivatives
	The Company is exposed to foreign exchange rate risks in the normal course of business. To manage a portion of the accounting exposure resulting from changes in foreign currency exchange rates, the Company enters into foreign exchange contracts to hedge monetary assets and liabilities that are denominated in currencies other than the U.S. dollar. These foreign exchange contracts are carried at fair value and are not designated as hedging instruments. Changes in the value of the derivative are recognized in other expense, net, along with an offsetting remeasurement gain or loss on the underlying foreign currency denominated assets or liabilities.
	As of March 30, 2014, the Company had foreign exchange forward contracts in place to hedge exposures in the euro, Japanese yen, and Australian dollar. As of March 30, 2014 and December 29, 2013, the total notional amounts of outstanding forward contracts in place for foreign currency purchases were approximately $74.7 million and $54.7 million, respectively.
	Reserve for Product 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 the adequacy of its warranty reserve 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.
	Revenue Recognition
	The Company’s revenue is generated primarily from the sale of products and services. Product revenue primarily consists of sales of instruments and consumables used in genetic analysis. Service and other revenue primarily consists of revenue generated from genotyping and sequencing services and instrument service contracts.
	The Company recognizes revenue when persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the seller’s price to the buyer is fixed or determinable, and collectibility is reasonably assured. In instances where final acceptance of the product or system is required, revenue is deferred until all the acceptance criteria have been met. All revenue is recorded net of any discounts.
	Revenue from product sales is recognized generally upon transfer of title to the customer, provided that no significant obligations remain and collection of the receivable is reasonably assured. Revenue from instrument service contracts is recognized as the services are rendered, typically evenly over the contract term. Revenue from genotyping and sequencing services is recognized when earned, which is generally at the time the genotyping or sequencing analysis data is made available to the customer or agreed upon milestones are reached.
	In order to assess whether the price is fixed or determinable, the Company evaluates whether refund rights exist. If there are refund rights or payment terms based on future performance, the Company defers revenue recognition until the price becomes fixed or determinable. The Company assesses collectibility based on a number of factors, including past transaction history with, and the creditworthiness of, the customer. If the Company determines that collection of a payment is not reasonably assured, revenue recognition is deferred until receipt of payment.
	The Company regularly enters into contracts where revenue is derived from multiple deliverables including products or services. These products or services are generally delivered within a short time frame, approximately three to six months, after the contract execution date. Revenue recognition for contracts with multiple deliverables is based on the individual units of accounting determined to exist in the contract. A delivered item is considered a separate unit of accounting when the delivered item has value to the customer on a stand-alone basis. Items are considered to have stand-alone value when they are sold separately by any vendor or when the customer could resell the item on a stand-alone basis. Consideration is allocated at the inception of the contract to all deliverables based on their relative selling price. The relative selling price for each deliverable is determined using vendor specific objective evidence (VSOE) of selling price or third-party evidence of selling price if VSOE does not exist. If neither VSOE nor third-party evidence exists, the Company uses its best estimate of the selling price for the deliverable.
	In order to establish VSOE of selling price, the Company must regularly sell the product or service on a standalone basis with a substantial majority priced within a relatively narrow range. VSOE of selling price is usually the midpoint of that range. If there are not a sufficient number of standalone sales and VSOE of selling price cannot be determined, then the Company considers whether third party evidence can be used to establish selling price. Due to the lack of similar products and services sold by other companies within the industry, the Company has rarely established selling price using third-party evidence. If neither VSOE nor third party evidence of selling price exists, the Company determines its best estimate of selling price using average selling prices over a rolling 12-month period coupled with an assessment of current market conditions. If the product or service has no history of sales or if the sales volume is not sufficient, the Company relies upon prices set by the Company’s pricing committee adjusted for applicable discounts. The Company recognizes revenue for delivered elements only when it determines there are no uncertainties regarding customer acceptance.
	In certain markets, the Company sells products and provides services to customers through distributors that specialize in life science products. In most sales through distributors, the product is delivered directly to customers. In cases where the product is delivered to a distributor, revenue recognition is deferred until acceptance is received from the distributor, and/or the end-user, if required by the applicable sales contract. The terms of sales transactions through distributors are consistent with the terms of direct sales to customers. These transactions are accounted for in accordance with the Company’s revenue recognition policy described herein.
	Net Income (Loss) per Share
	Basic net income (loss) per share is computed based on the weighted average number of common shares outstanding during the period. Diluted net income (loss) per share is computed based on the sum of the weighted average number of common shares and dilutive potential common shares outstanding during the period.
	Dilutive potential 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 the 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 net income (loss) per share (in thousands):
		Three Months Ended
		March 30,	March 31,
		2014	2013
	Weighted average shares outstanding	128,146	123,768
	Effect of dilutive potential common shares from:
	Convertible senior notes	5,518	—
	Equity awards	4,816	—
	Warrants	12,139	—
	Weighted average shares used in calculation of diluted net income (loss) per share	150,619	123,768
	Potentially dilutive shares excluded from calculation due to anti-dilutive effect	124	32,942

Balance_Sheet_Account_Details

Balance Sheet Account Details	3 Months Ended
	Mar. 30, 2014
Balance Sheet Account Details [Abstract]	'
Balance Sheet Account Details	'
	Balance Sheet Account Details
	Short-Term Investments
	The following is a summary of short-term investments (in thousands):
		March 30, 2014												December 29, 2013
		Amortized			Gross			Gross			Estimated			Amortized		Gross		Gross			Estimated
		Cost			Unrealized			Unrealized			Fair Value			Cost		Unrealized		Unrealized			Fair Value
					Gains			Losses								Gains		Losses
	Available-for-sale securities:
	Debt securities in government sponsored entities	$	81,077		$	26		$	(78	)	$	81,025		$	82,226	$	18	$	(101	)	$	82,143
	Corporate debt securities	427,130			284			(427		)	426,987			342,034		312		(376		)	341,970
	U.S. Treasury securities	65,211			70			(4		)	65,277			29,795		58		—			29,853
	Total available-for-sale securities	$	573,418		$	380		$	(509	)	$	573,289		$	454,055	$	388	$	(477	)	$	453,966
	As of March 30, 2014, the Company had 118 available-for-sale securities in a gross unrealized loss position which had been in such position for less than twelve months. There were no impairments considered other-than-temporary as it is more likely than not the Company will hold the securities until maturity or the recovery of the cost basis. The following table shows the fair values and the gross unrealized losses of such available-for-sale securities that were in an unrealized loss position for less than twelve months as of March 30, 2014 and December 29, 2013, aggregated by investment category (in thousands):
		March 30, 2014						December 29, 2013
		Estimated			Gross			Estimated			Gross
		Fair Value			Unrealized			Fair Value			Unrealized
					Losses						Losses
	Debt securities in government sponsored entities	$	53,076		$	(78	)	$	73,362		$	(101	)
	Corporate debt securities	197,841			(398		)	168,118			(373		)
	U.S. Treasury securities	15,117			(4		)	—			—
	Total	$	266,034		$	(480	)	$	241,480		$	(474	)
	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 March 30, 2014 were as follows (in thousands):
		Estimated
		Fair Value
	Due within one year	$	204,870
	After one but within five years	368,419
	Total	$	573,289
	Cost-Method Investments
	As of March 30, 2014 and December 29, 2013, the aggregate carrying amounts of the Company’s cost-method investments in non-publicly traded companies were $26.7 million and $22.1 million, respectively, which were included in other assets. During the three months ended March 31, 2013, the Company sold a cost-method investment and recognized a $6.1 million gain. The Company’s cost-method investments are assessed for impairment quarterly. No impairment loss was recorded during the three months ended March 30, 2014 or March 31, 2013. The Company 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.
	Headquarter Facility Exit Obligation
	Changes in the Company’s facility exit obligation related to its former headquarters lease during the three months ended March 30, 2014 and March 31, 2013 are as follows (in thousands):
		Three Months Ended
		March 30,			March 31,
		2014			2013
	Balance at beginning of period	$	38,218		$	45,352
	Additional facility exit obligation accrued	—			286
	Accretion of interest expense	595			471
	Cash payments	(1,633		)	(2,201		)
	Balance at end of period	$	37,180		$	43,908
	Warranties
	Changes in the Company’s reserve for product warranties during the three months ended March 30, 2014 and March 31, 2013 are as follows (in thousands):
		Three Months Ended
		March 30,			March 31,
		2014			2013
	Balance at beginning of period	$	10,407		$	10,136
	Additions charged to cost of revenue	4,192			5,421
	Repairs and replacements	(3,107		)	(4,751		)
	Balance at end of period	$	11,492		$	10,806
	Inventory
	Inventory consists of the following (in thousands):
		March 30,			December 29,
		2014			2013
	Raw materials	$	56,798		$	57,398
	Work in process	78,742			70,016
	Finished goods	28,691			26,685
	Total inventory	$	164,231		$	154,099
	Goodwill
	Changes in the Company’s goodwill balance during the three months ended March 30, 2014 are as follows (in thousands):
		Goodwill
	Balance as of December 29, 2013	$	723,061
	Purchase price allocation adjustments related to a prior year acquisition	198
	Balance as of March 30, 2014	$	723,259
Accrued Liabilities
Accrued liabilities consist of the following (in thousands):
	March 30,			December 29,
	2014			2013
Accrued compensation expenses	$	66,623		$	82,705
Deferred revenue, current portion	59,535			50,834
Accrued taxes payable	30,644			30,435
Customer deposits	14,312			13,569
Reserve for product warranties	11,492			10,407
Acquisition related contingent liability, current portion	6,950			6,719
Facility exit obligation, current portion	6,102			5,570
Other	19,634			18,881
Total accrued liabilities	$	215,292		$	219,120

Acquisitions

Acquisitions	3 Months Ended
	Mar. 30, 2014
Business Combinations [Abstract]	'
Acquisitions	'
	Acquisitions
	2013 Acquisitions
	On February 21, 2013, the Company acquired all of the outstanding capital stock of Verinata Health, Inc., a provider of non-invasive tests for the early identification of fetal chromosomal abnormalities. The aggregate purchase price was $396.3 million, including total cash payment of $339.3 million, $56.2 million in fair value of the contingent milestone payments of up to $100.0 million, $0.2 million in fair value of converted stock options attributed to pre-combination services, and $0.5 million in loss realized on settlement of preexisting relationships.
	Assumptions used to estimate the acquisition date fair value of the contingent consideration included discount rates ranging from 6% to 20%, volatility of 50%, risk-free rate of 0.26%, revenue projections, and the probability of achieving regulatory 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.
	During 2013, the Company also completed acquisitions of Advanced Liquid Logic Inc., a provider of liquid handling solutions, NextBio, a provider of clinical and genomic informatics tools, and another development-stage company. As a result of these transactions, the Company recorded $126.5 million in goodwill. The purchase price allocation for the NextBio acquisition is preliminary and subject to change as more detailed analyses are completed and additional information with respect to the fair values of the assets and liabilities acquired becomes available.
	2012 Acquisition
	On September 19, 2012, the Company announced the acquisition of BlueGnome Ltd., a provider of cytogenetics and in vitro fertilization screening products. Total consideration for the acquisition was $95.5 million, which included $88.0 million in initial cash payments and $7.5 million in fair value of contingent cash consideration of up to $20.0 million based on the achievement of certain revenue based milestones by December 28, 2014.
	Summary of Contingent Compensation Expenses
	Contingent compensation expenses recorded as a result of acquisitions consist of the following (in thousands):
		Three Months Ended
		March 30,		March 31,
		2014		2013
	Contingent compensation, included in research and development expense	$	83	$	489
	Contingent compensation, included in selling, general and administrative expense	2,756		2,929
	Total contingent compensation expense	$	2,839	$	3,418

Fair_Value_Measurements

Fair Value Measurements	3 Months Ended
	Mar. 30, 2014
Fair Value Disclosures [Abstract]	'
Fair Value Measurements	'
	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 March 30, 2014 and December 29, 2013 (in thousands):
		March 30, 2014									December 29, 2013
		Level 1			Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
	Assets:
	Money market funds (cash equivalents)	$	344,622		$	—	$	—	$	344,622	$	478,755	$	—	$	—	$	478,755
	Debt securities in government-sponsored entities	—			81,025		—		81,025		—		82,143		—		82,143
	Corporate debt securities	—			426,987		—		426,987		—		341,970		—		341,970
	U.S. Treasury securities	65,277			—		—		65,277		29,853		—		—		29,853
	Deferred compensation plan assets	—			21,580		—		21,580		—		17,805		—		17,805
	Total assets measured at fair value	$	409,899		$	529,592	$	—	$	939,491	$	508,608	$	441,918	$	—	$	950,526
	Liabilities:
	Acquisition related contingent consideration liabilities	$	—		$	—	$	47,720	$	47,720	$	—	$	—	$	49,480	$	49,480
	Deferred compensation liability	—			18,236		—		18,236		—		14,957		—		14,957
	Total liabilities measured at fair value	$	—		$	18,236	$	47,720	$	65,956	$	—	$	14,957	$	49,480	$	64,437
	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 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.
	The Company reassesses the fair value of contingent consideration to be settled in cash related to acquisitions on a quarterly basis using the income approach. This is a Level 3 measurement. Significant assumptions used in the measurement include probabilities of achieving the remaining milestones and the discount rates, which depend on the milestone risk profiles. The changes in the fair value of the contingent considerations during the three months ended March 30, 2014 were due to changes in the estimated payments and a shorter discounting period.
	Changes in estimated fair value of contingent consideration liabilities during the three months ended March 30, 2014 are as follows (in thousands):
		Contingent
		Consideration
		Liability
		(Level 3 Measurement)
	Balance as of December 29, 2013	$	49,480
	Change in estimated fair value, recorded in acquisition related (gain) expense, net	(1,760		)
	Balance as of March 30, 2014	$	47,720

Convertible_Senior_Notes

Convertible Senior Notes	3 Months Ended
	Mar. 30, 2014
Debt Disclosure [Abstract]	'
Convertible Senior Notes	'
	Convertible Senior Notes
	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). The Company pays 0.25% interest per annum on the principal amount of the 2016 Notes semiannually in arrears in cash on March 15 and September 15 of each year. The 2016 Notes mature on March 15, 2016. The effective rate of the liability component was estimated to be 4.5%.
	The 2016 Notes are 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 11.9687 shares per $1,000 principal amount of the 2016 Notes (which represents an initial conversion price of approximately $83.55 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 2016 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 March 31, 2011, 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 2016 Notes; and (4) at any time on or after December 15, 2015 through the second scheduled trading day immediately preceding the maturity date. During the three months ended March 30, 2014 and March 31, 2013, the 2016 Notes were not convertible. 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 and continue to be convertible through June 30, 2014.
	As noted in the indenture for the 2016 Notes, it is the Company’s intent and policy to settle conversions through combination settlement, which essentially involves repayment of an amount of cash equal to the “principal portion” and delivery of the “share amount” in excess of the conversion value over the principal portion in shares of common stock. As a policy election under applicable guidance related to the calculation of diluted net income per share, the Company elected the combination settlement method as its stated settlement policy and applied the treasury stock method in the calculation of the dilutive impact of the 2016 Notes. The calculation of dilutive potential common shares outstanding for the three months ended March 30, 2014 reflects the dilutive impact from the 2016 Notes. If the 2016 Notes were converted as of March 30, 2014, the if-converted value would exceed the principal amount by $817.8 million.
	0.625% Convertible Senior Notes due 2014
	In 2007, the Company issued $400.0 million principal amount of 0.625% convertible senior notes due 2014 (2014 Notes) with a maturity date of February 15, 2014. The effective interest rate of the liability component was estimated to be 8.3%.
	The 2014 Notes became convertible into cash and shares of the Company’s common stock in various prior periods and became convertible again from April 1, 2012 through, and including, February 12, 2014. All notes were converted by February 12, 2014. In all cases of conversions of the 2014 Notes, the principal amount converted was repaid with cash and the excess of the conversion value over the principal amount was paid in shares of common stock. The equity dilution resulting from the issuance of common stock related to the conversion of the 2014 Notes was offset by repurchase of the same amount of shares under the convertible note hedge transactions, which were automatically exercised in accordance with their terms at the time of each conversion.
	Upon conversion, the Company records losses 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 dates. To measure the fair value of the converted notes as of the settlement dates, the applicable interest rates were estimated using Level 2 observable inputs and applied to the converted notes using the same methodology utilized for the issuance date valuation.
	The following table summarizes information about the conversions of the 2014 Notes during the three months ended March 30, 2014 (in thousands):
		2014 Notes
	Cash paid for principal of notes converted	$	29,570
	Conversion value over principal amount paid in shares of common stock	$	196,095
	Number of shares of common stock issued upon conversion	1,151
	The following table summarizes information about the equity and liability components of the 2014 Notes and 2016 Notes (dollars in thousands). The fair values of the respective notes outstanding were measured based on quoted market prices.
		March 30,			December 29,
		2014			2013
	Principal amount of convertible notes outstanding	$	920,000		$	949,570
	Unamortized discount of liability component	(71,984		)	(80,977		)
	Net carrying amount of liability component	848,016			868,593
	Less: current portion	(848,016		)	(29,288		)
	Long-term debt	$	—		$	839,305
	Conversion option subject to cash settlement	—			$	282
	Carrying value of equity component, net of debt issuance cost	$	155,366		$	274,304
	Fair value of outstanding notes	$	1,635,903		$	1,428,743
	Weighted average remaining amortization period of discount on the liability component	1.9 years			2.2 years

Sharebased_Compensation_Expens

Share-based Compensation Expense	3 Months Ended
	Mar. 30, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Share-based Compensation Expense	'
	Share-based Compensation Expense
	Share-based compensation expense for all stock awards consists of the following (in thousands):
		Three Months Ended
		March 30,			March 31,
		2014			2013
	Cost of product revenue	$	2,095		$	1,442
	Cost of service and other revenue	285			154
	Research and development	11,669			8,006
	Selling, general and administrative	19,375			14,617
	Share-based compensation expense before taxes	33,424			24,219
	Related income tax benefits	(10,577		)	(7,565		)
	Share-based compensation expense, net of taxes	$	22,847		$	16,654
	The assumptions used for the specified reporting periods and the resulting estimates of weighted-average fair value per share for stock purchased under the ESPP during the three months ended March 30, 2014 are as follows:
		Employee Stock Purchase Rights
	Risk-free interest rate	0.07 - 0.11%
	Expected volatility	38		%
	Expected term	0.5 - 1.0 year
	Expected dividends	—
	Weighted average fair value per share	$	41.84
	As of March 30, 2014, approximately $237.4 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 2.2 years.

Stockholders_Equity

Stockholders' Equity	3 Months Ended
	Mar. 30, 2014
Equity [Abstract]	'
Stockholders' Equity	'
	Stockholders’ Equity
	As of March 30, 2014, approximately 6.5 million shares remained available for future grants under the 2005 Stock Plan, the 2005 Solexa Equity Plan, and the 2008 Verinata Health Stock Plan.
	Stock Options
	The Company’s stock option activity under all stock option plans during the three months ended March 30, 2014 is as follows:
		Options		Weighted-Average
		(in thousands)		Exercise Price
	Outstanding at December 29, 2013	5,724		$	32.64
	Exercised	(875	)	$	25.94
	Cancelled	(4	)	$	4.35
	Outstanding at March 30, 2014	4,845		$	33.87
	At March 30, 2014, outstanding options to purchase 4.0 million shares were exercisable with a weighted average exercise price per share of $33.64.
	Restricted Stock
	A summary of the Company’s restricted stock activity and related information for the three months ended March 30, 2014 is as follows:
		Restricted Stock Awards		Restricted Stock Units		Performance Stock Units		Weighted Average
		(RSA)		(RSU)		(PSU)		Grant-Date Fair Value per Share
								RSA		RSU		PSU
	Outstanding at December 29, 2013	248		3,628		1,101		$	53.46	$	59.66	$	54.64
	Awarded	—		222		187		—		$	141.49	$	147.3
	Vested	(123	)	(409	)	—		$	47.9	$	50.82	—
	Cancelled	—		(55	)	(10	)	—		$	53.79	$	49.04
	Outstanding at March 30, 2014	125		3,386		1,278		$	55.44	$	66.21	$	68.24
	Employee Stock Purchase Plan
	The price at which common stock is purchased under the Employee Stock Purchase Plan (ESPP) is equal to 85% of the fair market value of the common stock on the first or last day of the offering period, whichever is lower. During the three months ended March 30, 2014, approximately 0.2 million shares were issued under the ESPP. As of March 30, 2014, there were approximately 14.8 million shares available for issuance under the ESPP.
	Warrants
	In connection with the offering of the 2014 Notes, the Company sold warrants to purchase 18.3 million shares of common stock to counterparties to the convertible note hedge transactions. The warrants have an exercise price of $31.435 per share, and the proceeds from the sale of such warrants were used by the Company to partially offset the cost of the transactions. In July 2013, the Company settled with a hedging counterparty outstanding warrants to purchase approximately 3.0 million shares of the Company’s common stock for $125.0 million in cash. As of March 30, 2014 warrants to purchase 15.4 million shares of the Company’s common stock remained outstanding. All outstanding warrants will be exercised immediately prior to expiration, which occurs in equal installments during the 40 consecutive scheduled trading days beginning on May 16, 2014.
	Share Repurchases
	During the three months ended March 30, 2014 and March 31, 2013, the Company repurchased 0.8 million shares for $130.0 million and 0.5 million shares for $25.0 million, respectively.
	In April 2012 the Company’s Board of Directors authorized share repurchases for up to $250.0 million via a combination of Rule 10b5-1 and discretionary share repurchase programs. In addition, on January 30, 2014, the Company’s Board of Directors authorized up to $250.0 million to repurchase shares of the Company’s common stock on a discretionary basis. Authorizations to repurchase up to an additional $237.5 million of the Company’s common stock remained as of March 30, 2014.

Income_Taxes

Income Taxes	3 Months Ended
	Mar. 30, 2014
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 rate for the three months ended March 30, 2014 was 28.4%. The variance from the U.S. federal statutory tax rate of 35% was primarily attributable to a higher mix of foreign earnings, such as earnings in Singapore and the United Kingdom, taxed at rates lower than the U.S. federal statutory tax rate, and tax deductions related to stock award activities which were recorded as discrete items in the quarter. In 2013, the variance from the U.S. federal statutory tax rate was primarily attributable to a higher mix of foreign earnings taxed at rates lower than the U.S. federal statutory tax rate and the retroactive reinstatement of the federal research and development credit for 2012 which was enacted in January 2013.
	In May 2013, the Internal Revenue Service began an audit of the Company’s corporate income tax return filed for fiscal year 2011. The Internal Revenue Service continues to analyze the information provided by the Company and has not yet proposed any adjustments to the filed return.

Legal_Proceedings

Legal Proceedings	3 Months Ended
	Mar. 30, 2014
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 in outstanding litigations 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 November 24, 2010, Syntrix Biosystems, Inc. filed suit against the Company in the United States District Court for the Western District of Washington at Tacoma (Case No. C10-5870-BHS) alleging that the Company willfully infringed U.S. Patent No. 6,951,682 by selling its BeadChip array products, and that the Company misappropriated Syntrix’s trade secrets. On January 30, 2013, the Court granted the Company’s motion for summary judgment on Syntrix’s trade secret claims, and dismissed those claims from the case. On March 14, 2013, a jury reached a verdict in favor of Syntrix, finding that Illumina’s BeadChip kits infringe the Syntrix patent. During trial, the Court dismissed Syntrix’s claim that the alleged infringement was willful. On July 1, 2013, the Court entered a Final Amended Judgment for $115.1 million, in accordance with the jury verdict, including supplemental damages and prejudgment interest. In addition, the Court awarded Syntrix an ongoing royalty of 8% for accused sales from March 15, 2013 until the patent expires on September 16, 2019. The Company believes that it did not infringe the Syntrix patent and that the patent is invalid. Therefore, the Company disagrees with the judgment and contends that the judgment is not supported by the law or facts. Accordingly, on December 3, 2013, the Company filed a Notice of Appeal to the Court of Appeals for the Federal Circuit challenging the Final Amended Judgment. On December 16, 2013, Syntrix cross appealed the Court’s dismissal of its trade secret claims and denial of its willfulness claim.
	As a result of the amended judgment, the Company recorded a legal contingency accrual of $138.8 million and $132.9 million as of March 30, 2014 and December 29, 2013, respectively, including damages and interest awarded to Syntrix. In the three months ended March 30, 2014, the Company recorded a related charge of $5.8 million to cost of product revenue. In the three months ended March 31, 2013, the Company recorded charges of $106.9 million, with $105.9 million charged to operating expenses and the remainder to cost of product revenue. The judgment amount has been secured by a supersedeas bond, and as of March 30, 2014, $17.8 million was deposited with the Court for the accrued post-judgment ongoing royalty amounts. The Company will continue to deposit with the Court ongoing royalties on future sales at the royalty rate stated in the Final Amended Judgment during the appeal process. Funds deposited with the Court are reported as restricted cash in other long-term assets.

Summary_of_Significant_Account1

Summary of Significant Accounting Policies (Policies)	3 Months Ended
	Mar. 30, 2014
Accounting Policies [Abstract]	'
Basis of Presentation	'
	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. The unaudited condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries. 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.
	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 December 29, 2013, 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.
Segment Information	'
	Segment Information
	Effective December 30, 2013, the Company reorganized and separated the roles of the Chief Executive Officer and the President, with core market and operational functions centralized and reporting to the President for the primary purpose of achieving scalability in business operations to support the growth in its strategic markets. Corporate functions and the President report to the CEO. As a result, the Company operates under one operating segment and reports under one reportable segment.
Fiscal Year	'
	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 months ended March 30, 2014 and March 31, 2013 were both 13 weeks.
Derivatives	'
	Derivatives
	The Company is exposed to foreign exchange rate risks in the normal course of business. To manage a portion of the accounting exposure resulting from changes in foreign currency exchange rates, the Company enters into foreign exchange contracts to hedge monetary assets and liabilities that are denominated in currencies other than the U.S. dollar. These foreign exchange contracts are carried at fair value and are not designated as hedging instruments. Changes in the value of the derivative are recognized in other expense, net, along with an offsetting remeasurement gain or loss on the underlying foreign currency denominated assets or liabilities.
	As of March 30, 2014, the Company had foreign exchange forward contracts in place to hedge exposures in the euro, Japanese yen, and Australian dollar. As of March 30, 2014 and December 29, 2013, the total notional amounts of outstanding forward contracts in place for foreign currency purchases were approximately $74.7 million and $54.7 million, respectively
Reserve for Product Warranties	'
	Reserve for Product 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 the adequacy of its warranty reserve 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.
Revenue Recognition	'
	Revenue Recognition
	The Company’s revenue is generated primarily from the sale of products and services. Product revenue primarily consists of sales of instruments and consumables used in genetic analysis. Service and other revenue primarily consists of revenue generated from genotyping and sequencing services and instrument service contracts.
	The Company recognizes revenue when persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the seller’s price to the buyer is fixed or determinable, and collectibility is reasonably assured. In instances where final acceptance of the product or system is required, revenue is deferred until all the acceptance criteria have been met. All revenue is recorded net of any discounts.
	Revenue from product sales is recognized generally upon transfer of title to the customer, provided that no significant obligations remain and collection of the receivable is reasonably assured. Revenue from instrument service contracts is recognized as the services are rendered, typically evenly over the contract term. Revenue from genotyping and sequencing services is recognized when earned, which is generally at the time the genotyping or sequencing analysis data is made available to the customer or agreed upon milestones are reached.
	In order to assess whether the price is fixed or determinable, the Company evaluates whether refund rights exist. If there are refund rights or payment terms based on future performance, the Company defers revenue recognition until the price becomes fixed or determinable. The Company assesses collectibility based on a number of factors, including past transaction history with, and the creditworthiness of, the customer. If the Company determines that collection of a payment is not reasonably assured, revenue recognition is deferred until receipt of payment.
	The Company regularly enters into contracts where revenue is derived from multiple deliverables including products or services. These products or services are generally delivered within a short time frame, approximately three to six months, after the contract execution date. Revenue recognition for contracts with multiple deliverables is based on the individual units of accounting determined to exist in the contract. A delivered item is considered a separate unit of accounting when the delivered item has value to the customer on a stand-alone basis. Items are considered to have stand-alone value when they are sold separately by any vendor or when the customer could resell the item on a stand-alone basis. Consideration is allocated at the inception of the contract to all deliverables based on their relative selling price. The relative selling price for each deliverable is determined using vendor specific objective evidence (VSOE) of selling price or third-party evidence of selling price if VSOE does not exist. If neither VSOE nor third-party evidence exists, the Company uses its best estimate of the selling price for the deliverable.
	In order to establish VSOE of selling price, the Company must regularly sell the product or service on a standalone basis with a substantial majority priced within a relatively narrow range. VSOE of selling price is usually the midpoint of that range. If there are not a sufficient number of standalone sales and VSOE of selling price cannot be determined, then the Company considers whether third party evidence can be used to establish selling price. Due to the lack of similar products and services sold by other companies within the industry, the Company has rarely established selling price using third-party evidence. If neither VSOE nor third party evidence of selling price exists, the Company determines its best estimate of selling price using average selling prices over a rolling 12-month period coupled with an assessment of current market conditions. If the product or service has no history of sales or if the sales volume is not sufficient, the Company relies upon prices set by the Company’s pricing committee adjusted for applicable discounts. The Company recognizes revenue for delivered elements only when it determines there are no uncertainties regarding customer acceptance.
	In certain markets, the Company sells products and provides services to customers through distributors that specialize in life science products. In most sales through distributors, the product is delivered directly to customers. In cases where the product is delivered to a distributor, revenue recognition is deferred until acceptance is received from the distributor, and/or the end-user, if required by the applicable sales contract. The terms of sales transactions through distributors are consistent with the terms of direct sales to customers. These transactions are accounted for in accordance with the Company’s revenue recognition policy described herein.
Net Income (Loss) per Share	'
	Net Income (Loss) per Share
	Basic net income (loss) per share is computed based on the weighted average number of common shares outstanding during the period. Diluted net income (loss) per share is computed based on the sum of the weighted average number of common shares and dilutive potential common shares outstanding during the period.
	Dilutive potential 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 the 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 net income (loss) per share (in thousands):
		Three Months Ended
		March 30,	March 31,
		2014	2013
	Weighted average shares outstanding	128,146	123,768
	Effect of dilutive potential common shares from:
	Convertible senior notes	5,518	—
	Equity awards	4,816	—
	Warrants	12,139	—
	Weighted average shares used in calculation of diluted net income (loss) per share	150,619	123,768
	Potentially dilutive shares excluded from calculation due to anti-dilutive effect	124	32,942

Summary_of_Significant_Account2

Summary of Significant Accounting Policies (Tables)	3 Months Ended
	Mar. 30, 2014
Accounting Policies [Abstract]	'
Weighted average shares used to calculate basic and diluted net income (loss) per share	'
	The following table presents the calculation of weighted average shares used to calculate basic and diluted net income (loss) per share (in thousands):
		Three Months Ended
		March 30,	March 31,
		2014	2013
	Weighted average shares outstanding	128,146	123,768
	Effect of dilutive potential common shares from:
	Convertible senior notes	5,518	—
	Equity awards	4,816	—
	Warrants	12,139	—
	Weighted average shares used in calculation of diluted net income (loss) per share	150,619	123,768
	Potentially dilutive shares excluded from calculation due to anti-dilutive effect	124	32,942

Balance_Sheet_Account_Details_

Balance Sheet Account Details (Tables)	3 Months Ended
	Mar. 30, 2014
Balance Sheet Account Details [Abstract]	'
Short-term investments	'
	The following is a summary of short-term investments (in thousands):
		March 30, 2014												December 29, 2013
		Amortized			Gross			Gross			Estimated			Amortized		Gross		Gross			Estimated
		Cost			Unrealized			Unrealized			Fair Value			Cost		Unrealized		Unrealized			Fair Value
					Gains			Losses								Gains		Losses
	Available-for-sale securities:
	Debt securities in government sponsored entities	$	81,077		$	26		$	(78	)	$	81,025		$	82,226	$	18	$	(101	)	$	82,143
	Corporate debt securities	427,130			284			(427		)	426,987			342,034		312		(376		)	341,970
	U.S. Treasury securities	65,211			70			(4		)	65,277			29,795		58		—			29,853
	Total available-for-sale securities	$	573,418		$	380		$	(509	)	$	573,289		$	454,055	$	388	$	(477	)	$	453,966
Available-for-sale securities in unrealized loss positions	'
	The following table shows the fair values and the gross unrealized losses of such available-for-sale securities that were in an unrealized loss position for less than twelve months as of March 30, 2014 and December 29, 2013, aggregated by investment category (in thousands):
		March 30, 2014						December 29, 2013
		Estimated			Gross			Estimated			Gross
		Fair Value			Unrealized			Fair Value			Unrealized
					Losses						Losses
	Debt securities in government sponsored entities	$	53,076		$	(78	)	$	73,362		$	(101	)
	Corporate debt securities	197,841			(398		)	168,118			(373		)
	U.S. Treasury securities	15,117			(4		)	—			—
	Total	$	266,034		$	(480	)	$	241,480		$	(474	)
Contractual maturities of available-for-sale securities	'
	Contractual maturities of available-for-sale debt securities as of March 30, 2014 were as follows (in thousands):
		Estimated
		Fair Value
	Due within one year	$	204,870
	After one but within five years	368,419
	Total	$	573,289
Headquarter facility exit obligation	'
	Changes in the Company’s facility exit obligation related to its former headquarters lease during the three months ended March 30, 2014 and March 31, 2013 are as follows (in thousands):
		Three Months Ended
		March 30,			March 31,
		2014			2013
	Balance at beginning of period	$	38,218		$	45,352
	Additional facility exit obligation accrued	—			286
	Accretion of interest expense	595			471
	Cash payments	(1,633		)	(2,201		)
	Balance at end of period	$	37,180		$	43,908
Warranties	'
	Changes in the Company’s reserve for product warranties during the three months ended March 30, 2014 and March 31, 2013 are as follows (in thousands):
		Three Months Ended
		March 30,			March 31,
		2014			2013
	Balance at beginning of period	$	10,407		$	10,136
	Additions charged to cost of revenue	4,192			5,421
	Repairs and replacements	(3,107		)	(4,751		)
	Balance at end of period	$	11,492		$	10,806
Inventory	'
	Inventory consists of the following (in thousands):
		March 30,			December 29,
		2014			2013
	Raw materials	$	56,798		$	57,398
	Work in process	78,742			70,016
	Finished goods	28,691			26,685
	Total inventory	$	164,231		$	154,099
Goodwill	'
	Changes in the Company’s goodwill balance during the three months ended March 30, 2014 are as follows (in thousands):
		Goodwill
	Balance as of December 29, 2013	$	723,061
	Purchase price allocation adjustments related to a prior year acquisition	198
	Balance as of March 30, 2014	$	723,259
Accrued liabilities	'
	Accrued liabilities consist of the following (in thousands):
		March 30,			December 29,
		2014			2013
	Accrued compensation expenses	$	66,623		$	82,705
	Deferred revenue, current portion	59,535			50,834
	Accrued taxes payable	30,644			30,435
	Customer deposits	14,312			13,569
	Reserve for product warranties	11,492			10,407
	Acquisition related contingent liability, current portion	6,950			6,719
	Facility exit obligation, current portion	6,102			5,570
	Other	19,634			18,881
	Total accrued liabilities	$	215,292		$	219,120

Acquisitions_Tables

Acquisitions (Tables)	3 Months Ended
	Mar. 30, 2014
Business Combinations [Abstract]	'
Contingent compensation expenses	'
	Contingent compensation expenses recorded as a result of acquisitions consist of the following (in thousands):
		Three Months Ended
		March 30,		March 31,
		2014		2013
	Contingent compensation, included in research and development expense	$	83	$	489
	Contingent compensation, included in selling, general and administrative expense	2,756		2,929
	Total contingent compensation expense	$	2,839	$	3,418

Fair_Value_Measurements_Tables

Fair Value Measurements (Tables)	3 Months Ended
	Mar. 30, 2014
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 March 30, 2014 and December 29, 2013 (in thousands):
		March 30, 2014									December 29, 2013
		Level 1			Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
	Assets:
	Money market funds (cash equivalents)	$	344,622		$	—	$	—	$	344,622	$	478,755	$	—	$	—	$	478,755
	Debt securities in government-sponsored entities	—			81,025		—		81,025		—		82,143		—		82,143
	Corporate debt securities	—			426,987		—		426,987		—		341,970		—		341,970
	U.S. Treasury securities	65,277			—		—		65,277		29,853		—		—		29,853
	Deferred compensation plan assets	—			21,580		—		21,580		—		17,805		—		17,805
	Total assets measured at fair value	$	409,899		$	529,592	$	—	$	939,491	$	508,608	$	441,918	$	—	$	950,526
	Liabilities:
	Acquisition related contingent consideration liabilities	$	—		$	—	$	47,720	$	47,720	$	—	$	—	$	49,480	$	49,480
	Deferred compensation liability	—			18,236		—		18,236		—		14,957		—		14,957
	Total liabilities measured at fair value	$	—		$	18,236	$	47,720	$	65,956	$	—	$	14,957	$	49,480	$	64,437
Changes in estimated fair value of contingent consideration liabilities	'
	Changes in estimated fair value of contingent consideration liabilities during the three months ended March 30, 2014 are as follows (in thousands):
		Contingent
		Consideration
		Liability
		(Level 3 Measurement)
	Balance as of December 29, 2013	$	49,480
	Change in estimated fair value, recorded in acquisition related (gain) expense, net	(1,760		)
	Balance as of March 30, 2014	$	47,720

Convertible_Senior_Notes_Table

Convertible Senior Notes (Tables)	3 Months Ended
	Mar. 30, 2014
Debt Disclosure [Abstract]	'
Summarized information about the conversions during the period	'
	The following table summarizes information about the conversions of the 2014 Notes during the three months ended March 30, 2014 (in thousands):
		2014 Notes
	Cash paid for principal of notes converted	$	29,570
	Conversion value over principal amount paid in shares of common stock	$	196,095
	Number of shares of common stock issued upon conversion	1,151
Summarized information about equity and liability components of convertible senior notes	'
	The following table summarizes information about the equity and liability components of the 2014 Notes and 2016 Notes (dollars in thousands). The fair values of the respective notes outstanding were measured based on quoted market prices.
		March 30,			December 29,
		2014			2013
	Principal amount of convertible notes outstanding	$	920,000		$	949,570
	Unamortized discount of liability component	(71,984		)	(80,977		)
	Net carrying amount of liability component	848,016			868,593
	Less: current portion	(848,016		)	(29,288		)
	Long-term debt	$	—		$	839,305
	Conversion option subject to cash settlement	—			$	282
	Carrying value of equity component, net of debt issuance cost	$	155,366		$	274,304
	Fair value of outstanding notes	$	1,635,903		$	1,428,743
	Weighted average remaining amortization period of discount on the liability component	1.9 years			2.2 years

Sharebased_Compensation_Expens1

Share-based Compensation Expense (Tables)	3 Months Ended
	Mar. 30, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
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
		March 30,			March 31,
		2014			2013
	Cost of product revenue	$	2,095		$	1,442
	Cost of service and other revenue	285			154
	Research and development	11,669			8,006
	Selling, general and administrative	19,375			14,617
	Share-based compensation expense before taxes	33,424			24,219
	Related income tax benefits	(10,577		)	(7,565		)
	Share-based compensation expense, net of taxes	$	22,847		$	16,654
Assumptions used to estimate the fair value per share of employee stock purchase rights granted	'
	The assumptions used for the specified reporting periods and the resulting estimates of weighted-average fair value per share for stock purchased under the ESPP during the three months ended March 30, 2014 are as follows:
		Employee Stock Purchase Rights
	Risk-free interest rate	0.07 - 0.11%
	Expected volatility	38		%
	Expected term	0.5 - 1.0 year
	Expected dividends	—
	Weighted average fair value per share	$	41.84

Stockholders_Equity_Tables

Stockholders' Equity (Tables)	3 Months Ended
	Mar. 30, 2014
Equity [Abstract]	'
Stock option activity under all stock option plans	'
	The Company’s stock option activity under all stock option plans during the three months ended March 30, 2014 is as follows:
		Options		Weighted-Average
		(in thousands)		Exercise Price
	Outstanding at December 29, 2013	5,724		$	32.64
	Exercised	(875	)	$	25.94
	Cancelled	(4	)	$	4.35
	Outstanding at March 30, 2014	4,845		$	33.87
Restricted stock activity	'
	A summary of the Company’s restricted stock activity and related information for the three months ended March 30, 2014 is as follows:
		Restricted Stock Awards		Restricted Stock Units		Performance Stock Units		Weighted Average
		(RSA)		(RSU)		(PSU)		Grant-Date Fair Value per Share
								RSA		RSU		PSU
	Outstanding at December 29, 2013	248		3,628		1,101		$	53.46	$	59.66	$	54.64
	Awarded	—		222		187		—		$	141.49	$	147.3
	Vested	(123	)	(409	)	—		$	47.9	$	50.82	—
	Cancelled	—		(55	)	(10	)	—		$	53.79	$	49.04
	Outstanding at March 30, 2014	125		3,386		1,278		$	55.44	$	66.21	$	68.24

Summary_of_Significant_Account3

Summary of Significant Accounting Policies (Details)	3 Months Ended
In Thousands, unless otherwise specified	Mar. 30, 2014	Mar. 31, 2013
Weighted average shares used to calculate basic and diluted net income per share	'	'
Weighted average shares outstanding	128,146	123,768
Effect of dilutive potential common shares from:	'	'
Convertible senior notes	5,518	'
Equity awards	4,816	'
Warrants	12,139	'
Weighted average shares used in calculation of diluted net income (loss) per share	150,619	123,768
Potentially dilutive shares excluded from calculation due to anti-dilutive effect	124	32,942

Summary_of_Significant_Account4

Summary of Significant Accounting Policies (Details Textual) (USD $)	3 Months Ended
In Millions, unless otherwise specified	Mar. 30, 2014	Mar. 31, 2013	Dec. 29, 2013
	segments
Number of Operating Segments	1	'	'
Number of Reportable Segments	1	'	'
Quarterly Operating Cycle (in weeks)	'P13W	'P13W	'
Total notional amount of outstanding forward contract in place for foreign currency purchase	$74.70	'	$54.70
Instrument warranty period	'1 year	'	'
Period of time average selling prices are observed to establish best estimate of selling price	'12 months	'	'
Minimum [Member]	'	'	'
Warranty on Consumable Sales Through the Expiration Date	'6 months	'	'
Product or service delivery period	'3 months	'	'
Maximum [Member]	'	'	'
Warranty on Consumable Sales Through the Expiration Date	'12 months	'	'
Product or service delivery period	'6 months	'	'

Balance_Sheet_Account_Details_1

Balance Sheet Account Details (Details) (USD $)	Mar. 30, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	$573,418	$454,055
Available for sale securities, Gross Unrealized Gains	380	388
Available for sale securities, Gross Unrealized Losses	-509	-477
Available for sale securities, Estimated fair value	573,289	453,966
Debt securities in government sponsored entities [Member]	'	'
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	81,077	82,226
Available for sale securities, Gross Unrealized Gains	26	18
Available for sale securities, Gross Unrealized Losses	-78	-101
Available for sale securities, Estimated fair value	81,025	82,143
Corporate debt securities [Member]	'	'
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	427,130	342,034
Available for sale securities, Gross Unrealized Gains	284	312
Available for sale securities, Gross Unrealized Losses	-427	-376
Available for sale securities, Estimated fair value	426,987	341,970
U.S. Treasury securities [Member]	'	'
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	65,211	29,795
Available for sale securities, Gross Unrealized Gains	70	58
Available for sale securities, Gross Unrealized Losses	-4	'
Available for sale securities, Estimated fair value	$65,277	$29,853

Balance_Sheet_Account_Details_2

Balance Sheet Account Details (Details 1) (USD $)	Mar. 30, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	$266,034	$241,480
Available For Sale Securities Gross Unrealized Loss Accumulated in Investments	-480	-474
Debt securities in government sponsored entities [Member]	'	'
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	53,076	73,362
Available For Sale Securities Gross Unrealized Loss Accumulated in Investments	-78	-101
Corporate debt securities [Member]	'	'
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	197,841	168,118
Available For Sale Securities Gross Unrealized Loss Accumulated in Investments	-398	-373
U.S. Treasury securities [Member]	'	'
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	15,117	'
Available For Sale Securities Gross Unrealized Loss Accumulated in Investments	($4)	'

Balance_Sheet_Account_Details_3

Balance Sheet Account Details (Details 2) (USD $)	Mar. 30, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Available-for-sale Securities, Debt Maturities, Fair Value, Fiscal Year Maturity [Abstract]	'	'
Due within one year	$204,870	'
After one but within five years	368,419	'
Available for sale securities, Estimated fair value	$573,289	$453,966

Balance_Sheet_Account_Details_4

Balance Sheet Account Details (Details 3) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Mar. 30, 2014	Mar. 31, 2013
Headquarter Facility Exit Obligation [Roll Forward]	'	'
Balance at the beginning of the period	$38,218	$45,352
Additional facility exit obligation accrued	0	286
Accretion of interest expense	595	471
Cash payments	-1,633	-2,201
Balance at the end of the period	$37,180	$43,908

Balance_Sheet_Account_Details_5

Balance Sheet Account Details (Details 4) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Mar. 30, 2014	Mar. 31, 2013
Reserve for product warranties [Roll Forward]	'	'
Balance as of beginning of period	$10,407	$10,136
Additions charged to cost of revenue	4,192	5,421
Repairs and replacements	-3,107	-4,751
Balance as of end of period	$11,492	$10,806

Balance_Sheet_Account_Details_6

Balance Sheet Account Details (Details 5) (USD $)	Mar. 30, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Inventory [Abstract]	'	'
Raw materials	$56,798	$57,398
Work in process	78,742	70,016
Finished goods	28,691	26,685
Total inventory	$164,231	$154,099

Balance_Sheet_Account_Details_7

Balance Sheet Account Details (Details 6) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Mar. 30, 2014
Goodwill [Roll Forward]	'
Balance as of beginning of period	$723,061
Purchase price allocation adjustments related to a prior year acquisition	198
Balance as of end of period	$723,259

Balance_Sheet_Account_Details_8

Balance Sheet Account Details (Details 7) (USD $)	Mar. 30, 2014	Dec. 29, 2013	Mar. 31, 2013	Dec. 30, 2012
In Thousands, unless otherwise specified
Accrued Liabilities, Current [Abstract]	'	'	'	'
Accrued compensation expenses	$66,623	$82,705	'	'
Deferred revenue, current portion	59,535	50,834	'	'
Accrued taxes payable	30,644	30,435	'	'
Customer deposits	14,312	13,569	'	'
Reserve for product warranties	11,492	10,407	10,806	10,136
Acquisition related contingent liability, current portion	6,950	6,719	'	'
Facility exit obligation, current portion	6,102	5,570	'	'
Other	19,634	18,881	'	'
Total accrued liabilities	$215,292	$219,120	'	'

Balance_Sheet_Account_Details_9

Balance Sheet Account Details (Details Textual) (USD $)	3 Months Ended
	Mar. 31, 2013	Mar. 30, 2014	Dec. 29, 2013
		securities
Balance Sheet Account Details [Abstract]	'	'	'
Number of available-for-sale securities in a gross unrealized loss position (in securities)	'	118	'
Company's cost-method investments in non-publicly traded company	'	$26,700,000	$22,100,000
Cost-method investment related gain	$6,113,000	'	'

Acquisitions_Details

Acquisitions (Details) (Contingent compensation expense [Member], USD $)	3 Months Ended
In Thousands, unless otherwise specified	Mar. 30, 2014	Mar. 31, 2013
Business Combination, Separately Recognized Transactions [Line Items]	'	'
Contingent compensation expense	$2,839	$3,418
Research and Development Expense [Member]	'	'
Business Combination, Separately Recognized Transactions [Line Items]	'	'
Contingent compensation expense	83	489
Selling, general and administrative [Member]	'	'
Business Combination, Separately Recognized Transactions [Line Items]	'	'
Contingent compensation expense	$2,756	$2,929

Acquisitions_Details_Textual

Acquisitions (Details Textual) (USD $)	Mar. 30, 2014	Dec. 29, 2013	Feb. 21, 2013	Dec. 29, 2013	Sep. 19, 2012	Feb. 21, 2013	Feb. 21, 2013
			Verinata [Member]	Series of Individually Immaterial Business Acquisitions [Member]	BlueGnome [Member]	Minimum [Member]	Maximum [Member]
						Verinata [Member]	Verinata [Member]
Acquisition [Abstract]	'	'	'	'	'	'	'
Business Combination, Consideration Transferred	'	'	$396,300,000	'	$95,500,000	'	'
Business acquisition cash consideration	'	'	339,300,000	'	88,000,000	'	'
Fair value of contingent consideration to be settled in cash	'	'	56,200,000	'	7,500,000	'	'
Contingent consideration payments, maximum	'	'	100,000,000	'	20,000,000	'	'
Fair value of assumed equity attributed to pre-combination services	'	'	200,000	'	'	'	'
Loss realized on settlement of preexisting relationships	'	'	-500,000	'	'	'	'
Fair value inputs, discount rate	'	'	'	'	'	6.00%	20.00%
Fair value assumptions, expected volatility rate	'	'	50.00%	'	'	'	'
Fair value assumptions, risk free interest rate	'	'	0.26%	'	'	'	'
Goodwill	$723,259,000	$723,061,000	'	$126,500,000	'	'	'

Fair_Value_Measurements_Detail

Fair Value Measurements (Details) (USD $)

3 Months Ended

3 Months Ended

In Thousands, unless otherwise specified

Mar. 30, 2014

Mar. 31, 2013

Mar. 30, 2014

Dec. 29, 2013

Mar. 30, 2014

Dec. 29, 2013

Mar. 30, 2014

Dec. 29, 2013

Mar. 30, 2014

Mar. 30, 2014

Dec. 29, 2013

Mar. 30, 2014

Dec. 29, 2013

Mar. 30, 2014

Dec. 29, 2013

Mar. 30, 2014

Dec. 29, 2013

Mar. 30, 2014

Dec. 29, 2013

Mar. 30, 2014

Dec. 29, 2013

Mar. 30, 2014

Dec. 29, 2013

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Inputs, Level 1 [Member]

Fair Value, Inputs, Level 1 [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Inputs, Level 3 [Member]

Fair Value, Inputs, Level 3 [Member]

Fair Value, Inputs, Level 3 [Member]

Debt securities in government sponsored entities [Member]

Debt securities in government sponsored entities [Member]

Debt securities in government sponsored entities [Member]

Debt securities in government sponsored entities [Member]

Corporate debt securities [Member]

Corporate debt securities [Member]

Corporate debt securities [Member]

Corporate debt securities [Member]

U.S. Treasury securities [Member]

U.S. Treasury securities [Member]

U.S. Treasury securities [Member]

U.S. Treasury securities [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Inputs, Level 2 [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Inputs, Level 1 [Member]

Fair Value, Inputs, Level 1 [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Fair Value, Measurements, Recurring [Member]

Assets:

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Money market funds (cash equivalents)

'

'

$344,622

$478,755

$344,622

$478,755

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Investments, fair value disclosure

'

'

'

'

'

'

'

'

'

'

'

81,025

82,143

81,025

82,143

426,987

341,970

426,987

341,970

65,277

29,853

65,277

29,853

Deferred compensation plan assets

'

'

21,580

17,805

'

'

21,580

17,805

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Total assets measured at fair value

'

'

939,491

950,526

409,899

508,608

529,592

441,918

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Liabilities:

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Acquisition related contingent consideration liability

'

'

47,720

49,480

'

'

'

'

47,720

47,720

49,480

'

'

'

'

'

'

'

'

'

'

'

'

Deferred compensation liability

'

'

18,236

14,957

'

'

18,236

14,957

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Total liabilities measured at fair value

'

'

65,956

64,437

'

'

18,236

14,957

'

47,720

49,480

'

'

'

'

'

'

'

'

'

'

'

'

Change in estimated fair value of the contingent consideration liability

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Balance as of beginning of period

'

'

47,720

49,480

'

'

'

'

49,480

47,720

49,480

'

'

'

'

'

'

'

'

'

'

'

'

Change in estimated fair value, recorded in acquisition related (gain) expense, net

-1,760

464

'

'

'

'

'

'

-1,760

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Balance as of end of period

'

'

$47,720

$49,480

'

'

'

'

$47,720

$47,720

$49,480

'

'

'

'

'

'

'

'

'

'

'

'

Convertible_Senior_Notes_Detai

Convertible Senior Notes (Details) (0.625% Convertible Senior Notes due 2014 [Member], USD $)	3 Months Ended
In Thousands, unless otherwise specified	Mar. 30, 2014
0.625% Convertible Senior Notes due 2014 [Member]	'
Extinguishment of Debt [Line Items]	'
Cash paid for principal of notes converted	$29,570
Conversion value over principal amount paid in shares of common stock	$196,095
Number of shares of common stock issued upon conversion	1,151

Convertible_Senior_Notes_Detai1

Convertible Senior Notes (Details 1) (USD $)	Mar. 30, 2014	Dec. 29, 2013
In Thousands, unless otherwise specified
Summarized information about equity and liability components of convertible senior notes	'	'
Principal amount of convertible notes outstanding	$920,000	$949,570
Unamortized discount of liability component	-71,984	-80,977
Net carrying amount of liability component	848,016	868,593
Less: current portion	-848,016	-29,288
Long-term debt	0	839,305
Conversion option subject to cash settlement	'	282
Carrying value of equity component, net of debt issuance cost	155,366	274,304
Fair value of outstanding notes	$1,635,903	$1,428,743
Weighted average remaining amortization period of discount on the liability component	'1 year 11 months	'2 years 2 months

Convertible_Senior_Notes_Detai2

Convertible Senior Notes (Details Textual) (USD $)	3 Months Ended	12 Months Ended	3 Months Ended	12 Months Ended
	Mar. 30, 2014	Jan. 01, 2012	Mar. 30, 2014	Dec. 30, 2007
	0.25% Convertible Senior Notes due 2016 [Member]	0.25% Convertible Senior Notes due 2016 [Member]	0.625% Convertible Senior Notes due 2014 [Member]	0.625% Convertible Senior Notes due 2014 [Member]
Debt Instrument [Line Items]	'	'	'	'
Issuance of convertible senior notes	'	$920,000,000	'	$400,000,000
Interest rate on convertible senior notes	'	0.25%	'	0.63%
Debt Instrument, Maturity Date	'	15-Mar-16	'	15-Feb-14
Effective interest rates of liability component	'	4.50%	'	8.30%
Conversion rate per $1,000 principal amount of notes (in shares per thousand dollars)	'	11.9687	'	'
Principal amount used in calculating incremental share settlement amount	'	1,000	'	'
Conversion price (in dollars per share)	'	$83.55	'	'
Circumstances of converting notes at referred conversion ratio	'	'(1) during the five business-day period after any 10 consecutive trading day period (the “measurement period”) in which the trading price per 2016 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 March 31, 2011, 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 2016 Notes; and (4) at any time on or after December 15, 2015 through the second scheduled trading day immediately preceding the maturity date.	'	'
Number of consecutive trading days on which trading price is examined for triggering of conversion (in days)	'	'30 days	'	'
Number of consecutive trading days in the measurement period (in days)	'	'10 days	'	'
Conversion triggering common stock trading price as a percentage of price last reported in Measurement period converted at conversion rate	'	'less than 98%	'	'
Number of days in which common stock prices needed to exceed triggering price in order to trigger conversion (in days)	'	'20 or more	'	'
Conversion triggering common stock price as a percentage of applicable conversion price in effect on the last trading day of the immediately preceding calendar quarter	'	'exceeds 130%	'	'
Date after which notes will become convertible at any time	'	15-Dec-15	'	'
Convertible senior note conversion start period	1-Apr-14	'	1-Apr-12	'
Convertible senior note conversion end period	30-Jun-14	'	12-Feb-14	'
If-converted value in excess of principal	$817,800,000	'	'	'

Sharebased_Compensation_Expens2

Share-based Compensation Expense (Details) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Mar. 30, 2014	Mar. 31, 2013
Share-based Compensation	'	'
Share-based compensation expense before taxes	$33,424	$24,219
Related income tax benefits	-10,577	-7,565
Share-based compensation expense, net of taxes	22,847	16,654
Cost of product revenue	'	'
Share-based Compensation	'	'
Share-based compensation expense before taxes	2,095	1,442
Cost of service and other revenue	'	'
Share-based Compensation	'	'
Share-based compensation expense before taxes	285	154
Research and development	'	'
Share-based Compensation	'	'
Share-based compensation expense before taxes	11,669	8,006
Selling, general and administrative	'	'
Share-based Compensation	'	'
Share-based compensation expense before taxes	$19,375	$14,617

Sharebased_Compensation_Expens3

Share-based Compensation Expense (Details 1) (Employee Stock Purchase Rights [Member], USD $)	3 Months Ended
	Mar. 30, 2014
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'
Risk-free interest rate, minimum	0.07%
Risk-free interest rate, maximum	0.11%
Expected volatility	38.00%
Expected dividends	0.00%
Weighted average fair value per share (in dollars per share)	$41.84
Minimum [Member]	'
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'
Expected term (in years)	'6 months
Maximum [Member]	'
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'
Expected term (in years)	'1 year

Sharebased_Compensation_Expens4

Share-based Compensation Expense (Details Textual) (USD $)	3 Months Ended
In Millions, unless otherwise specified	Mar. 30, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Unrecognized compensation cost related to stock options, restricted stock units and ESPP shares issued to date	$237.40
Weighted-average period of unrecognized compensation cost related to stock options, restricted stock units and ESPP shares issued to date (in years)	'2 years 2 months

Stockholders_Equity_Details

Stockholders' Equity (Details) (USD $)	3 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Mar. 30, 2014
Stock option activity	'
Outstanding at period start (in shares)	5,724
Options, Exercised (in shares)	-875
Options, Cancelled (in shares)	-4
Outstanding at period end (in shares)	4,845
Weighted-Average Exercise Price, Outstanding at beginning of period (in dollars per share)	$32.64
Weighted Average Exercise Price, Exercised (in dollars per share)	$25.94
Weighted Average Exercise Price, Cancelled (in dollars per share)	$4.35
Weighted-Average Exercise Price, Outstanding at end of period (in dollars per share)	$33.87

Stockholders_Equity_Details_1

Stockholders' Equity (Details 1) (USD $)	3 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Mar. 30, 2014
Restricted Stock [Member]	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Outstanding at period start (in shares)	248
Vested (in shares)	-123
Outstanding at period end (in shares)	125
Weighted Average Grant Date Fair Value per Share, Outstanding at period start (in dollars per share)	$53.46
Weighted Average Grant Date Fair Value per Share, Vested (in dollars per share)	$47.90
Weighted Average Grant Date Fair Value per Share, Outstanding at period end (in dollars per share)	$55.44
Restricted Stock Units (RSUs) [Member]	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Outstanding at period start (in shares)	3,628
Awarded (in shares)	222
Vested (in shares)	-409
Cancelled (in shares)	-55
Outstanding at period end (in shares)	3,386
Weighted Average Grant Date Fair Value per Share, Outstanding at period start (in dollars per share)	$59.66
Weighted Average Grant Date Fair Value per Share, Awarded (in dollars per share)	$141.49
Weighted Average Grant Date Fair Value per Share, Vested (in dollars per share)	$50.82
Weighted Average Grant Date Fair Value per Share, Cancelled (in dollars per share)	$53.79
Weighted Average Grant Date Fair Value per Share, Outstanding at period end (in dollars per share)	$66.21
Performance Shares [Member]	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Outstanding at period start (in shares)	1,101
Awarded (in shares)	187
Cancelled (in shares)	-10
Outstanding at period end (in shares)	1,278
Weighted Average Grant Date Fair Value per Share, Outstanding at period start (in dollars per share)	$54.64
Weighted Average Grant Date Fair Value per Share, Awarded (in dollars per share)	$147.30
Weighted Average Grant Date Fair Value per Share, Cancelled (in dollars per share)	$49.04
Weighted Average Grant Date Fair Value per Share, Outstanding at period end (in dollars per share)	$68.24

Stockholders_Equity_Details_Te

Stockholders' Equity (Details Textual) (USD $)	1 Months Ended	3 Months Ended		0 Months Ended				3 Months Ended
Share data in Millions, except Per Share data, unless otherwise specified	Jul. 28, 2013	Mar. 30, 2014	Mar. 31, 2013	Jan. 30, 2014	Apr. 18, 2013	16-May-14	Dec. 30, 2007	Mar. 30, 2014	Mar. 30, 2014
				January 30 2014 Stock Repurchase Program [Member]	April 18, 2012 Stock Repurchase Plan [Member]	Warrant [Member]	Warrant [Member]	Employee Stock Purchase Plan [Member]	2005 Illumina, Solexa, and Verinata Plans [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'	'	'	'	'	'
Shares available for issuance	'	'	'	'	'	'	'	14.8	6.5
Stock options exercisable (in shares)	'	4	'	'	'	'	'	'	'
Stock options exercisable outstanding weighted average exercise price per share (in dollars per share)	'	$33.64	'	'	'	'	'	'	'
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	'	'	'	'	'	'	'	0.2	'
Class of Warrant or Right, Number of Securities Called by Warrants or Rights	'	15.4	'	'	'	'	18.3	'	'
Class of Warrant or Right, Exercise Price of Warrants or Rights1	'	'	'	'	'	'	$31.43	'	'
Class of Warrant or Right, Number of Securities Called by Warrants or Rights, Settled in Period	3	'	'	'	'	'	'	'	'
(Payments for) proceeds from warrant settlements	($125,000,000)	'	'	'	'	'	'	'	'
Warrant Expiration Period	'	'	'	'	'	'40 days	'	'	'
Treasury Stock, Shares, Acquired	'	0.8	0.5	'	'	'	'	'	'
Common stock repurchases	'	130,017,000	25,011,000	'	'	'	'	'	'
Stock Repurchase Program, Authorized Amount	'	'	'	250,000,000	250,000,000	'	'	'	'
Stock Repurchase Program, Remaining Authorized Repurchase Amount 1	'	$237,500,000	'	'	'	'	'	'	'

Income_Taxes_Details_Textual

Income Taxes (Details Textual)	3 Months Ended
	Mar. 30, 2014
Income Tax Disclosure [Abstract]	'
Effective tax rate	28.40%
U.S. statutory rate	35.00%

Legal_Proceedings_Details_Text

Legal Proceedings (Details Textual) (USD $)	3 Months Ended			0 Months Ended	3 Months Ended		3 Months Ended
	Mar. 31, 2013	Mar. 30, 2014	Dec. 29, 2013	Jul. 02, 2013	Mar. 31, 2013	Mar. 30, 2014	Mar. 30, 2014	Mar. 31, 2013
				Syntrix [Member]	Syntrix [Member]	Syntrix [Member]	Syntrix [Member]	Syntrix [Member]
							Cost of Sales [Member]	Operating Expense [Member]
Loss Contingencies [Line Items]	'	'	'	'	'	'	'	'
Legal contingencies, damages awarded	'	'	'	$115,100,000	'	'	'	'
Loss contingency, damages awarded, royalty rate	'	'	'	8.00%	'	'	'	'
Long-term legal contingencies	'	138,780,000	132,933,000	'	'	'	'	'
Legal contingencies	105,853,000	'	'	'	106,900,000	'	5,800,000	105,900,000
Restricted Cash and Cash Equivalents, Noncurrent	'	'	'	'	'	$17,800,000	'	'