Illumina (ILMN) 10-K 18 Feb 14 2013 FY Annual report Financial data

Document_and_Entity_Informatio

Document and Entity Information Document (USD $)	12 Months Ended
Share data in Millions, unless otherwise specified	Dec. 29, 2013	Jan. 31, 2014	Jun. 30, 2013
Document and Entity Information [Abstract]	'	'	'
Entity Registrant Name	'Illumina Inc	'	'
Entity Central Index Key	'0001110803	'	'
Current Fiscal Year End Date	'--12-29	'	'
Entity Filer Category	'Large Accelerated Filer	'	'
Document Type	'10-K	'	'
Document Period End Date	29-Dec-13	'	'
Document Fiscal Year Focus	'2013	'	'
Document Fiscal Period Focus	'FY	'	'
Amendment Flag	'false	'	'
Entity Common Stock, Shares Outstanding	'	128.2	'
Entity Well-known Seasoned Issuer	'Yes	'	'
Entity Voluntary Filers	'No	'	'
Entity Current Reporting Status	'Yes	'	'
Entity Public Float	'	'	$6,900,000,000

Consolidated_Balance_Sheets

Consolidated Balance Sheets (USD $)	Dec. 29, 2013	Dec. 30, 2012
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$711,637	$433,981
Short-term investments	453,966	916,223
Accounts receivable, net	238,946	214,975
Inventory	154,099	158,718
Deferred tax assets, current portion	36,076	30,451
Prepaid expenses and other current assets	22,811	32,700
Total current assets	1,617,535	1,787,048
Property and equipment, net	202,666	166,167
Goodwill	723,061	369,327
Intangible assets, net	331,173	130,196
Deferred tax assets, long-term portion	88,480	40,183
Other assets	56,091	73,164
Total assets	3,019,006	2,566,085
Current liabilities:	'	'
Accounts payable	73,655	65,727
Accrued liabilities	219,120	201,877
Long-term debt, current portion	29,288	36,967
Total current liabilities	322,063	304,571
Long-term debt	839,305	805,406
Long-term legal contingencies	132,933	'
Other long-term liabilities	191,221	134,369
Commitments and contingencies	'	'
Conversion option subject to cash settlement	282	3,158
Stockholders' equity:	'	'
Preferred stock: $0.01 par value, 10,000 shares authorized; no shares issued and outstanding at December 29, 2013 and December 30, 2012	0	0
Common stock, $0.01 par value, 320,000 shares authorized; 175,205 shares issued and 127,723 outstanding at December 29, 2013; 170,171 shares issued and 123,943 outstanding at December 30, 2012	1,753	1,703
Additional paid-in capital	2,562,705	2,419,831
Accumulated other comprehensive income	1,234	2,123
Retained earnings	207,855	82,547
Treasury stock, 47,482 shares and 46,228 shares at cost at December 29, 2013 and December 30, 2012, respectively	-1,240,345	-1,187,623
Total stockholders’ equity	1,533,202	1,318,581
Total liabilities and stockholders’ equity	$3,019,006	$2,566,085

Consolidated_Balance_Sheets_Pa

Consolidated Balance Sheets (Parenthetical) (USD $)	Dec. 29, 2013	Dec. 30, 2012
In Thousands, except Per Share data, unless otherwise specified
Statement of Financial Position [Abstract]	'	'
Common stock, par value	$0.01	$0.01
Common stock, shares authorized	320,000	320,000
Common stock, shares issued	175,205	170,171
Common stock, shares outstanding	127,723	123,943
Preferred stock, par value	$0.01	$0.01
Preferred stock, shares authorized	10,000	10,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Treasury stock, shares	47,482	46,228

Consolidated_Statements_of_Inc

Consolidated Statements of Income (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Revenue:	'	'	'
Product revenue	$1,264,656	$1,055,826	$987,280
Service and other revenue	156,522	92,690	68,255
Total revenue	1,421,178	1,148,516	1,055,535
Cost of revenue:	'	'	'
Cost of product revenue	407,877	317,283	308,228
Cost of service and other revenue	67,811	43,552	26,118
Amortization of acquired intangible assets	33,603	14,153	12,091
Total cost of revenue	509,291	374,988	346,437
Gross profit	911,887	773,528	709,098
Operating expense:	'	'	'
Research and development	276,743	231,025	196,913
Selling, general and administrative	381,040	285,991	261,843
Legal contingencies	115,369	'	'
Unsolicited tender offer related expense	13,621	23,136	'
Acquisition related (gain) expense, net	-11,617	2,774	919
Headquarter relocation	2,624	26,328	41,826
Restructuring	'	3,522	8,136
Total operating expense	777,780	572,776	509,637
Income from operations	134,107	200,752	199,461
Other income (expense):	'	'	'
Interest income	4,887	16,208	7,052
Interest expense	-39,690	-37,779	-34,790
Cost-method investment related gain, net	61,357	45,911	'
Other expense, net	-1,347	-2,484	-38,678
Total other income (expense), net	25,207	21,856	-66,416
Income before income taxes	159,314	222,608	133,045
Provision for income taxes	34,006	71,354	46,417
Net income	$125,308	$151,254	$86,628
Net income per basic share	$1	$1.23	$0.70
Net income per diluted share	$0.90	$1.13	$0.62
Shares used in calculating basic net income per share	125,076	122,999	123,399
Shares used in calculating diluted net income per share	139,936	133,693	138,937

Consolidated_Statements_of_Com

Consolidated Statements of Comprehensive Income (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Statement of Comprehensive Income [Abstract]	'	'	'
Net income	$125,308	$151,254	$86,628
Unrealized (loss) gain on available-for-sale securities, net of deferred tax	-889	6	352
Total comprehensive income	$124,419	$151,260	$86,980

Consolidated_Statements_of_Sto

Consolidated Statements of Stockholders' Equity (USD $)	Total	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Other Comprehensive Income [Member]	Retained Earnings (Accumulated Deficit) [Member]	Treasury Stock [Member]
In Thousands, unless otherwise specified
Balance at Jan. 02, 2011	$1,197,675	$1,516	$1,891,288	$1,765	($155,335)	($541,559)
Balance, shares at Jan. 02, 2011	'	151,513	'	'	'	-24,904
Increase (Decrease) in Stockholders' Equity [Roll Forward]	'	'	'	'	'	'
Net income	86,628	'	'	'	86,628	'
Unrealized (loss) gain on available-for-sale securities, net of deferred tax	352	'	'	352	'	'
Issuance of common stock, net of repurchases, shares	'	15,194	'	'	'	-19,990
Stock issued during period, net of repurchases	-467,787	152	104,268	'	'	-572,207
Convertible note, equity portion, net of tax and issuance costs	155,366	'	155,366	'	'	'
Tax impact from the issuance of convertible debt	-59,427	'	-59,427	'	'	'
Tax benefit related to conversions of convertible debt	11,409	'	11,409	'	'	'
Reclassification of conversion option subject to cash settlement	7,667	'	7,667	'	'	'
Share-based compensation	92,153	'	92,153	'	'	'
Net incremental tax benefit related to share-based compensation	43,122	'	43,122	'	'	'
Equity based contingent compensation	3,457	'	3,457	'	'	'
Issuance of treasury stock, shares	'	'	'	'	'	229
Issuance of treasury stock, value	4,600	'	597	'	'	4,003
Balance at Jan. 01, 2012	1,075,215	1,668	2,249,900	2,117	-68,707	-1,109,763
Balance, shares at Jan. 01, 2012	'	166,707	'	'	'	-44,665
Increase (Decrease) in Stockholders' Equity [Roll Forward]	'	'	'	'	'	'
Net income	151,254	'	'	'	151,254	'
Unrealized (loss) gain on available-for-sale securities, net of deferred tax	6	'	'	6	'	'
Issuance of common stock, net of repurchases, shares	'	3,464	'	'	'	-1,875
Stock issued during period, net of repurchases	-28,165	35	55,106	'	'	-83,306
Reclassification of conversion option subject to cash settlement	2,565	'	2,565	'	'	'
Share-based compensation	94,385	'	94,385	'	'	'
Net incremental tax benefit related to share-based compensation	17,015	'	17,015	'	'	'
Equity based contingent compensation	6,306	'	6,306	'	'	'
Issuance of treasury stock, shares	'	'	'	'	'	312
Issuance of treasury stock, value	'	'	-5,446	'	'	5,446
Balance at Dec. 30, 2012	1,318,581	1,703	2,419,831	2,123	82,547	-1,187,623
Balance, shares at Dec. 30, 2012	'	170,171	'	'	'	-46,228
Increase (Decrease) in Stockholders' Equity [Roll Forward]	'	'	'	'	'	'
Net income	125,308	'	'	'	125,308	'
Unrealized (loss) gain on available-for-sale securities, net of deferred tax	-889	'	'	-889	'	'
Issuance of common stock, net of repurchases, shares	'	5,034	'	'	'	-1,254
Stock issued during period, net of repurchases	45,543	50	98,215	'	'	-52,722
Reclassification of conversion option subject to cash settlement	2,338	'	2,338	'	'	'
Share-based compensation	105,771	'	105,771	'	'	'
Net incremental tax benefit related to share-based compensation	53,032	'	53,032	'	'	'
Equity based contingent compensation	8,278	'	8,278	'	'	'
Fair value of options assumed in acquisition	240	'	240	'	'	'
Warrant retirement	-125,000	'	-125,000	'	'	'
Balance at Dec. 29, 2013	$1,533,202	$1,753	$2,562,705	$1,234	$207,855	($1,240,345)
Balance, shares at Dec. 29, 2013	'	175,205	'	'	'	-47,482

Consolidated_Statements_of_Cas

Consolidated Statements of Cash Flows (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Cash flows from operating activities:	'	'	'
Net income	$125,308	$151,254	$86,628
Adjustments to reconcile net income to net cash provided by operating activities:	'	'	'
Depreciation expense	50,810	48,249	55,575
Amortization of intangible assets	47,115	17,070	13,617
Share-based compensation expense	105,826	94,324	92,092
Accretion of debt discount	36,237	35,004	32,173
Change in facility exit obligation	2,624	22,367	23,638
Contingent compensation expense	8,278	6,306	3,457
Incremental tax benefit related to share-based compensation	-56,678	-20,783	-46,354
Deferred income taxes	-36,663	-21,698	19,227
Change in fair value of contingent consideration	-18,784	1,975	-4,500
Cost-method investment related gain, net	-61,357	-45,911	'
Impairments	25,214	21,438	'
Loss on extinguishment of debt	555	'	37,611
Other	4,533	251	9,949
Changes in operating assets and liabilities:	'	'	'
Accounts receivable	-15,928	-34,441	-7,011
Inventory	6,217	-23,707	22,152
Prepaid expenses and other current assets	1,783	-3,062	-2,016
Other assets	-16,357	-2,903	-4,004
Accounts payable	2,389	15,112	-21,097
Accrued liabilities	38,550	24,388	38,945
Long-term legal contingencies	132,933	'	'
Other long-term liabilities	3,816	6,640	8,058
Net cash provided by operating activities	386,421	291,873	358,140
Cash flows from investing activities:	'	'	'
Purchases of available-for-sale securities	-364,001	-925,478	-1,310,269
Sales of available-for-sale securities	523,635	498,371	568,447
Maturities of available-for-sale securities	289,197	400,379	492,444
Net cash paid for acquisitions	-523,501	-83,156	-58,302
Proceeds from (purchases of) strategic investments	95,580	40,881	-13,769
Purchases of property and equipment	-79,215	-68,781	-77,800
Cash paid for intangible assets	-11,344	-12,228	-1,750
Net cash used in investing activities	-69,649	-150,012	-400,999
Cash flows from financing activities:	'	'	'
Payments on current portion of long-term debt	-10,852	'	-349,874
Payments on acquisition related contingent consideration liability	-3,985	-3,374	'
Proceeds from issuance of convertible notes	'	'	903,492
Incremental tax benefit related to share-based compensation	56,678	20,783	46,354
Common stock repurchases	-50,020	-82,522	-570,406
(Payments for) proceeds from warrant settlements	-125,000	'	5,512
Proceeds from issuance of common stock	94,460	54,358	61,938
Net cash (used in) provided by financing activities	-38,719	-10,755	97,016
Effect of exchange rate changes on cash and cash equivalents	-397	-103	-126
Net increase in cash and cash equivalents	277,656	131,003	54,031
Cash and cash equivalents at beginning of year	433,981	302,978	248,947
Cash and cash equivalents at end of year	711,637	433,981	302,978
Supplemental cash flow information:	'	'	'
Cash paid for income taxes	50,086	74,037	9,806
Unsettled short-term investments purchase	'	$9,154	'

Organization_and_Summary_of_Si

Organization and Summary of Significant Accounting Policies	12 Months Ended
	Dec. 29, 2013
Organization and Summary of Significant Accounting Policies [Abstract]	'
Organization and Summary of Significant Accounting Policies	'
	Organization and Summary of Significant Accounting Policies
	Organization and Business
	Illumina, Inc. is a leading developer, manufacturer, and marketer of life science tools and integrated systems for the analysis of genetic variation and function. Using its proprietary technologies, Illumina provides innovative sequencing- and array-based solutions for genotyping, copy-number variation analysis, methylation studies, and gene expression profiling of DNA and RNA. The Company’s customers include leading genomic research centers, academic institutions, government laboratories, hospitals, and reference laboratories, as well as pharmaceutical, biotechnology, agrigenomics, commercial molecular diagnostic, and consumer genomics companies.
	Basis of Presentation
	The consolidated financial statements of the Company have been prepared in conformity with U.S. generally accepted accounting principles and include the accounts of the Company and its wholly-owned subsidiaries. All intercompany transactions and balances have been eliminated in consolidation.
	Fiscal Year
	The Company’s fiscal year is 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. Each of the years ended December 29, 2013, December 30, 2012, and January 1, 2012 were 52 weeks.
	Use of Estimates
	The preparation of financial statements requires that management make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue, expenses, and related disclosures of contingent assets and liabilities. Actual results could differ from those estimates.
	Segment Information
	For fiscal year 2013 and prior, the Company was organized in two operating segments for purposes of recording and reporting its financial results: Life Sciences and Diagnostics. The Life Sciences operating segment included all products and services related to the research market, namely the product lines based on the Company’s sequencing, BeadArray, and real-time polymerase chain reaction (PCR) technologies. The Diagnostics operating segment focused on the clinical and personalized application of the Company’s products and services for such uses as diagnosing disease, identifying genetic abnormalities, and identifying effective treatment therapies, with an initial emphasis on reproductive health and cancer. During all periods presented, the Diagnostics operating segment was immaterial to the financial statements as a whole. Accordingly, the financial results for both operating segments have been reported on an aggregate basis as one reportable segment.
	In late 2013, the Company announced organizational changes effective December 30, 2013 for the primary purpose of achieving scalability in business operations to support the growth in its strategic markets. The Company separated the roles of the Chief Executive Officer and the President, with core market and operational functions centralized and reporting to the President. Corporate functions and the President report to the CEO. As a result, the Company began operations as one operating segment as of December 30, 2013, and will continue to report under one reportable segment.
	Concentrations of Risk
	The Company operates in markets that are highly competitive and rapidly changing. Significant technological changes, shifting customer needs, the emergence of competitive products or services with new capabilities, and other factors could negatively impact the Company’s operating results. A significant portion of the Company’s customers consist of university and research institutions that management believes are, to some degree, directly or indirectly supported by the United States Government. A significant change in current research funding, particularly with respect to the National Institutes of Health, could have a material adverse impact on the Company’s future revenues and results of operations.
	The Company is also subject to risks related to its financial instruments including its cash and cash equivalents, investments, and accounts receivable. Most of the Company’s cash and cash equivalents as of December 29, 2013 were deposited with U.S. financial institutions, either domestically or with their foreign branches. The Company’s investment policy restricts the amount of credit exposure to any one issuer to 5% of the portfolio at the time of purchase and to any one industry sector, as defined by Bloomberg classifications, to 25% of the portfolio at the time of purchase. There is no limit to the percentage of the portfolio that may be maintained in U.S. Treasury securities, debt securities in U.S. government-sponsored entities, and money market funds.
	The Company’s products require customized products and components that currently are available from a limited number of sources. The Company sources certain key products and components included in its products from single vendors.
	The Company performs a regular review of customer activity and associated credit risks and does not require collateral or enter into netting arrangements. Shipments to customers outside the United States comprised 50%, 51%, and 50% of the Company’s revenue for the years ended December 29, 2013, December 30, 2012, and January 1, 2012, respectively. Customers outside the United States represented 52% and 54% of the Company’s gross trade accounts receivable balance as of December 29, 2013 and December 30, 2012, respectively.
	International sales entail a variety of risks, including currency exchange fluctuations, longer payment cycles, and greater difficulty in accounts receivable collection. The Company is also subject to general geopolitical risks, such as political, social and economic instability, and changes in diplomatic and trade relations. The risks of international sales are mitigated in part by the extent to which sales are geographically distributed. The Company has historically not experienced significant credit losses from investments and accounts receivable. Approximately 18% of the Company’s revenue is derived from European countries other than the United Kingdom. As the credit and economic conditions in certain southern European countries continue to deteriorate, the Company regularly reviews its outstanding accounts receivables in these countries and assesses the allowance for doubtful accounts accordingly. As of December 29, 2013, outstanding accounts receivables beyond standard payment terms from these countries accounted for less than 5% of the Company’s accounts receivable balance, and the Company has not experienced significant difficulties in collecting the accounts receivable outstanding in these countries.
	Fair Value Measurements
	The Company determines the fair value of its assets and liabilities based on the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. Valuation techniques used to measure fair value maximize the use of observable inputs and minimize the use of unobservable inputs. The Company uses a fair value hierarchy with three levels of inputs, of which the first two are considered observable and the last unobservable, to measure fair value:
	•	Level 1 — Quoted prices in active markets for identical assets or liabilities.
	•	Level 2 — Inputs, other than Level 1, that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.
	•	Level 3 — Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.
	The carrying amounts of financial instruments such as cash and cash equivalents, accounts receivable, prepaid expenses and other current assets, accounts payable, and accrued liabilities, excluding acquisition related contingent consideration liabilities, approximate the related fair values due to the short-term maturities of these instruments.
	Functional Currency
	The U.S. dollar is the functional currency of the Company’s international operations. The Company remeasures its foreign subsidiaries’ monetary assets and liabilities to the U.S. dollar and records the net gains or losses resulting from remeasurement in other expense, net in the consolidated statements of income.
	Acquisitions
	The Company measures all assets acquired and liabilities assumed, including contingent considerations and all contractual contingencies, at fair value as of the acquisition date. Contingent purchase considerations to be settled in cash are remeasured to estimated fair value at each reporting period with the change in fair value recorded in acquisition related (gain) expense, net, a component of operating expenses. In addition, the Company capitalizes in-process research and development (IPR&D) and either amortizes it over the life of the product upon commercialization, or impairs it if the project is abandoned. Post-acquisition adjustments in deferred tax asset valuation allowances and liabilities for uncertain tax positions are recorded in current period income tax expense.
	Cash Equivalents and Short-Term Investments
	Cash equivalents are comprised of short-term, highly liquid investments with maturities of 90 days or less at the date of purchase.
	Short-term investments consist of U.S. Treasury securities, debt securities in U.S. government-sponsored entities, and corporate debt securities. Management classifies short-term investments as available-for-sale at the time of purchase and evaluates such classification as of each balance sheet date. All short-term investments are recorded at estimated fair value. Unrealized gains and losses for available-for-sale securities are included in accumulated other comprehensive income, a component of stockholders’ equity. The Company evaluates its investments to assess whether those with unrealized loss positions are other than temporarily impaired. Impairments are considered to be other than temporary if they are related to deterioration in credit risk or if it is likely that the Company will sell the securities before the recovery of their cost basis. Realized gains, losses, and declines in value judged to be other than temporary are determined based on the specific identification method and are reported in other income (expense), net in the consolidated statements of income.
	Accounts Receivable
	Trade accounts receivable are recorded at the net invoice value and are not interest bearing. The Company considers receivables past due based on the contractual payment terms. The Company reserves specific receivables if collectibility is no longer reasonably assured. The Company also reserves a percentage of its trade receivable balance based on collection history and current economic trends that might impact the level of future credit losses. The Company re-evaluates such reserves on a regular basis and adjusts its reserves as needed. Once a receivable is deemed to be uncollectible, such balance is charged against the reserve.
	Inventory
	Inventory is stated at the lower of cost or market, on a first in, first out basis. Inventory includes raw materials and finished goods that may be used in the research and development process and such items are expensed as consumed or expired. Provisions for slow moving, excess, and obsolete inventories are estimated based on product life cycles, quality issues, historical experience, and usage forecasts.
	Property and Equipment
	Property and equipment are stated at cost, subject to review of impairment, and depreciated over the estimated useful lives of the assets, which generally range from three to seven years, using the straight-line method. Amortization of leasehold improvements is recorded over the shorter of the lease term or the estimated useful life of the related assets. Maintenance and repairs are charged to operations as incurred. When assets are sold, or otherwise disposed of, the cost and related accumulated depreciation are removed from the accounts and any gain or loss is included in operating expense.
	Leases
	Leases are reviewed and classified as capital or operating at their inception. The Company records rent expense on a straight-line basis over the term of the lease, which includes the construction build-out period and lease extension periods, if appropriate. The difference between rent payments and straight-line rent expense is recorded as deferred rent in accrued liabilities and other long-term liabilities. Landlord allowances are amortized on a straight-line basis over the lease term as a reduction to rent expense. The Company capitalizes leasehold improvements and amortizes the value over the shorter of the lease term or expected useful lives.
	Headquarter relocation expenses consisted of expenses such as accelerated depreciation expense, impairment of assets, additional rent expense during the transition period when both the new and former headquarter facilities were occupied, moving expenses, cease-use losses, and accretion of interest expense on lease exit liability.
	In 2012, the Company completed the relocation of its headquarters to another facility in San Diego, California. The Company recorded accelerated depreciation expense for leasehold improvements at its former headquarter facility based on the reassessed useful lives of less than a year. The Company recorded cease-use losses and the corresponding facility exit obligation upon vacating its former headquarters, calculated as the present value of the remaining lease obligation offset by estimated sublease rental receipts during the remaining lease period, adjusted for deferred items and estimated lease incentives. The key assumptions used in the calculation include the amount and timing of estimated sublease rental receipts, and the risk-adjusted discount rate.
	Goodwill, Intangible Assets and Other Long-Lived Assets
	Goodwill, which has an indefinite useful life, represents the excess of cost over fair value of net assets acquired. The change in the carrying value of goodwill during the year ended December 29, 2013 was due to goodwill recorded in connection with acquisitions. Goodwill is reviewed for impairment at least annually during the second quarter, or more frequently if an event occurs indicating the potential for impairment. During its goodwill impairment review, the Company may assess qualitative factors to determine whether it is more likely than not that the fair value of its reporting unit is less than its carrying amount, including goodwill. The qualitative factors include, but are not limited to, macroeconomic conditions, industry and market considerations, and the overall financial performance of the Company. If, after assessing the totality of these qualitative factors, the Company determines that it is not more likely than not that the fair value of its reporting unit is less than its carrying amount, then no additional assessment is deemed necessary. Otherwise, the Company proceeds to perform the two-step test for goodwill impairment. The first step involves comparing the estimated fair value of the reporting unit with its carrying value, including goodwill. If the carrying amount of the reporting unit exceeds its fair value, the Company performs the second step of the goodwill impairment test to determine the amount of loss, which involves comparing the implied fair value of the goodwill to the carrying value of the goodwill. The Company may also elect to bypass the qualitative assessment in a period and elect to proceed to perform the first step of the goodwill impairment test. The Company performed its annual assessment for goodwill impairment in the second quarter of 2013, noting no impairment.
	IPR&D, which also has an indefinite useful life, is reviewed for impairment at least annually, or more frequently if an event occurs indicating the potential for impairment. The IPR&D impairment test requires the Company to assess the fair value of the asset as compared to its carrying value and record an impairment charge if the carrying value exceeds the fair value. During the second fiscal quarter of 2012, the Company recorded $21.4 million in impairment charges of IPR&D within research and development expenses in the consolidated statements of income, when resources previously assigned to the research project were re-directed with no plans for additional investments to be made to the project in the foreseeable future.
	The Company’s identifiable intangible assets are typically comprised of acquired core technologies, licensed technologies, customer relationships, and trade names. The cost of identifiable intangible assets with finite lives is generally amortized on a straight-line basis over the assets’ respective estimated useful lives.
	The Company regularly performs reviews to determine if any event has occurred that may indicate its intangible assets with finite useful lives and other long-lived assets are potentially impaired. If indicators of impairment exist, the Company performs an impairment test to assess the recoverability of the affected assets by determining whether the carrying amount of such assets exceeds the undiscounted expected future cash flows. If the affected assets are not recoverable, the Company estimates the fair value of the assets and records an impairment loss if the carrying value of the assets exceeds the fair value. Factors that may indicate potential impairment include a significant decline in the Company’s stock price and market capitalization compared to its net book value, significant changes in the ability of a particular asset to generate positive cash flows the Company’s strategic business objectives, and the pattern of utilization of a particular asset.
	During 2013, the Company decided to discontinue its Eco and NuPCR product lines to better align its product portfolio with its core strategy. As a result, the Company recorded a total impairment charge of $25.2 million in cost of product revenue, $22.9 million of which related to identifiable intangible assets, including developed technology and license agreements.
	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 derivatives 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 December 29, 2013, the Company had foreign exchange forward contracts in place to hedge exposures in the euro, Japanese yen, and Australian dollar. As of December 29, 2013 and December 30, 2012, the total notional amount of outstanding forward contracts in place for foreign currency purchases was $54.7 million and $51.2 million, respectively. Non-designated foreign exchange forward contract related gain was $3.5 million for the year ended December 29, 2013 and immaterial for the years ended December 30, 2012 and January 1, 2012.
	Reserve for Product Warranties
	The Company generally provides a one-year warranty on instruments. Additionally, the Company provides a warranty on its 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 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 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.
	During the fiscal year ended January 1, 2012, the Company completed its Genome Analyzer trade-in program that enabled certain Genome Analyzer customers to trade in their Genome Analyzer and receive a discount on the purchase of a HiSeq 2000. The incentive was limited to customers who had purchased a Genome Analyzer prior to the beginning of the incentive program in early 2010 and was the only significant trade-in program offered by the Company.  The Company accounted for HiSeq 2000 discounts related to the Genome Analyzer trade-in program as reductions to revenue upon recognition of the HiSeq 2000 sales revenue, which is later than the date the trade-in program was launched.
	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.
	Share-Based Compensation
	The Company uses the Black-Scholes-Merton option-pricing model to estimate the fair value of stock options granted and stock purchases under the Employee Stock Purchase Plan (ESPP). This model incorporates various assumptions including expected volatility, expected term of an award, expected dividends, and the risk-free interest rates. The Company determines the expected volatility by equally weighing the historical and implied volatility of the Company’s common stock. The historical volatility of the Company’s common stock over the most recent period is generally commensurate with the estimated expected term of the Company’s stock awards, adjusted for the impact of unusual fluctuations not reasonably expected to recur and other relevant factors. The implied volatility is calculated from the implied market volatility of exchange-traded call options on the Company’s common stock. The expected term of an award is based on historical forfeiture experience, exercise activity, and on the terms and conditions of the stock awards. The expected dividend yield is determined to be 0% given that the Company has never declared or paid cash dividends on its common stock and does not anticipate paying such cash dividends. The risk-free interest rate is based upon U.S. Treasury securities with remaining terms similar to the expected term of the share-based awards. The fair value of restricted stock units granted is based on the closing market price of the Company’s common stock on the date of grant. The Company recognizes the fair value of share-based compensation on a straight-line basis over the requisite service periods of the awards.
Shipping and Handling Expenses
Shipping and handling expenses are included in cost of product revenue.
Research and Development
Research and development expenses include personnel expenses, contractor fees, license fees, facilities costs, and utilities. Expenditures relating to research and development are expensed in the period incurred.
Advertising Costs
The Company expenses advertising costs as incurred. Advertising costs were $14.5 million, $10.5 million, and $9.4 million for the years ended December 29, 2013, December 30, 2012, and January 1, 2012, respectively.
Restructuring Charges
During the year ended January 1, 2012, the Company announced and executed a restructuring plan to reduce the Company’s workforce and to consolidate certain facilities. The Company measured and accrued the liabilities associated with employee separation costs at fair value as of the date the plan was announced and terminations were communicated to employees, which primarily consisted of severance pay and other separation costs such as outplacement services and benefits.
The fair value measurement of restructuring related liabilities requires certain assumptions and estimates to be made by the Company, such as the retention period of certain employees, the timing and amount of sublease income on properties to be vacated, and the operating costs to be paid until lease termination. It is the Company’s policy to use the best estimates based on facts and circumstances available at the time of measurement, review the assumptions and estimates periodically, and adjust the liabilities when necessary.
Income Taxes
The provision for income taxes is computed using the asset and liability method, under which deferred tax assets and liabilities are recognized for the expected future tax consequences of temporary differences between the financial reporting and tax bases of assets and liabilities, and for the expected future tax benefit to be derived from tax loss and credit carryforwards. Deferred tax assets and liabilities are determined using the enacted tax rates in effect for the years in which those tax assets are expected to be realized. The effect of a change in tax rates on deferred tax assets and liabilities is recognized in the provision for income taxes in the period that includes the enactment date.
Deferred tax assets are regularly assessed to determine the likelihood they will be recovered from future taxable income. A valuation allowance is established when the Company believes it is more likely than not the future realization of all or some of a deferred tax asset will not be achieved. In evaluating the ability to recover deferred tax assets within the jurisdiction which they arise the Company considers all available positive and negative evidence. Factors reviewed include the cumulative pre-tax book income for the past three years, scheduled reversals of deferred tax liabilities, history of earnings and reliable forecasting, projections of pre-tax book income over the foreseeable future, and the impact of any feasible and prudent tax planning strategies.
The Company recognizes excess tax benefits associated with share-based compensation to stockholders’ equity only when realized. When assessing whether excess tax benefits relating to share-based compensation have been realized, the Company follows the with-and-without approach excluding any indirect effects of the excess tax deductions. Under this approach, excess tax benefits related to share-based compensation are not deemed to be realized until after the utilization of all other tax benefits available to the Company.
The Company recognizes the impact of a tax position in the financial statements only if that position is more likely than not of being sustained upon examination by taxing authorities, based on the technical merits of the position. Any interest and penalties related to uncertain tax positions will be reflected in income tax expense.
Net Income per Share
Basic net income per share is computed based on the weighted average number of common shares outstanding during the period. Diluted net income 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 therefore excluded.
The following table presents the calculation of weighted average number of shares used to calculate basic and diluted net income per share (in thousands):
	Years Ended
	December 29,			December 30,			January 1,
	2013			2012			2012
Weighted average shares outstanding	125,076			122,999			123,399
Effect of dilutive potential common shares from:
Convertible senior notes	1,340			967			3,783
Equity awards	4,404			3,906			4,703
Warrants	9,116			5,821			7,052
Weighted average shares used in calculating diluted net income per share	139,936			133,693			138,937
Potentially dilutive shares excluded from calculation due to anti-dilutive effect	996			2,556			2,418
Accumulated Other Comprehensive Income
Comprehensive income is comprised of net income and other comprehensive income. Accumulated other comprehensive income on the consolidated balance sheets at December 29, 2013 and December 30, 2012 includes accumulated foreign currency translation adjustments and unrealized gains and losses on the Company’s available-for-sale securities.
The components of accumulated other comprehensive income are as follows (in thousands):
	December 29,				December 30,
	2013				2012
Foreign currency translation adjustments	$	1,289			$	1,289
Unrealized (loss) gain on available-for-sale securities, net of deferred tax	(55		)		834
Total accumulated other comprehensive income	$	1,234			$	2,123

Balance_Sheet_Account_Details

Balance Sheet Account Details	12 Months Ended
	Dec. 29, 2013
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):
		December 29, 2013												December 30, 2012
					Gross			Gross								Gross		Gross
		Amortized			Unrealized			Unrealized			Estimated			Amortized		Unrealized		Unrealized			Estimated
		Cost			Gains			Losses			Fair Value			Cost		Gains		Losses			Fair Value
	Available-for-sale securities:
	Debt securities in government-sponsored entities	$	82,226		$	18		$	(101	)	$	82,143		$	314,638	$	251	$	(16	)	$	314,873
	Corporate debt securities	342,034			312			(376		)	341,970			471,989		1,059		(187		)	472,861
	U.S. Treasury securities	29,795			58			—			29,853			128,256		233		—			128,489
	Total available-for-sale securities	$	454,055		$	388		$	(477	)	$	453,966		$	914,883	$	1,543	$	(203	)	$	916,223
	As of December 29, 2013, the Company had 111 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 estimated fair values and the gross unrealized losses of the Company’s available-for-sale securities that were in an unrealized loss position for less than twelve months as of December 29, 2013 and December 30, 2012, respectively, aggregated by investment category (in thousands):
		December 29, 2013						December 30, 2012
		Estimated Fair Value			Gross			Estimated Fair Value			Gross
					Unrealized						Unrealized
					Losses						Losses
	Debt securities in government-sponsored entities	$	73,362		$	(101	)	$	28,176		$	(16	)
	Corporate debt securities	168,118			(373		)	130,224			(187		)
	Total	$	241,480		$	(474	)	$	158,400		$	(203	)
	Realized gains and losses are determined based on the specific identification method and are reported in interest income. To conform to the current year classification, the Company reclassified in the consolidated statements of cash flows, $235.0 million and $332.4 million of callable bonds redeemed prior to maturity from sales to maturities of available-for-sale securities for the years ended December 30, 2012 and January 1, 2012, respectively.
	Contractual maturities of available-for-sale debt securities as of December 29, 2013 are as follows (in thousands):
		Estimated Fair Value
	Due within one year	$	127,081
	After one but within five years	326,885
	Total	$	453,966
	Cost-Method Investments
	As of December 29, 2013 and December 30, 2012, the aggregate carrying amounts of the Company’s cost-method investments in non-publicly traded companies were $22.1 million and $56.3 million, respectively, which were included in other assets. The Company’s cost-method investments are assessed for impairment quarterly. The Company does not estimate 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.
	During the year ended December 29, 2013, the Company recorded cost-method investment related gains of $61.4 million, of which $55.2 million related to the sale of the Company’s minority interest in Oxford Nanopore Technologies Ltd. During the year ended December 30, 2012, the Company recorded $48.6 million in a gain from the sale of its minority ownership interest in deCODE Genetics, Inc. and $6.0 million in interest income from the recovery of a previously impaired loan from an investee.
	No impairment losses were recorded during the years ended December 29, 2013 and January 1, 2012. During the year ended December 30, 2012, the Company determined that a cost-method investment was other-than-temporarily impaired and recorded an impairment loss of $2.7 million. This determination was based upon operational performance trends coupled with uncertainty regarding the entity’s ability to obtain additional funding in a required timeframe for the entity to continue operations.
	Accounts Receivable
	Accounts receivable consist of the following (in thousands):
		December 29,			December 30,
		2013			2012
	Accounts receivable from product and service sales	$	241,360		$	217,369
	Other receivables	1,266			1,886
	Total accounts receivable, gross	242,626			219,255
	Allowance for doubtful accounts	(3,680		)	(4,280		)
	Total accounts receivable, net	$	238,946		$	214,975
	Inventory
	Inventory consists of the following (in thousands):
		December 29,			December 30,
		2013			2012
	Raw materials	$	57,398		$	61,665
	Work in process	70,016			75,675
	Finished goods	26,685			21,378
	Total inventory	$	154,099		$	158,718
	Property and Equipment
	Property and equipment, net consists of the following (in thousands):
		December 29,			December 30,
		2013			2012
	Leasehold improvements	$	104,571		$	87,734
	Machinery and equipment	175,340			158,112
	Computer hardware and software	73,544			58,313
	Furniture and fixtures	10,511			8,022
	Building	7,670			—
	Construction in progress	8,531			7,390
	Total property and equipment, gross	380,167			319,571
	Accumulated depreciation	(177,501		)	(153,404		)
	Total property and equipment, net	$	202,666		$	166,167
	Capital expenditures included accrued expenditures of $5.9 million for the year ended January 1, 2012. This amount has been excluded from the consolidated statements of cash flows. Accrued capital expenditures were immaterial for the years ended December 29, 2013, and December 30, 2012.
	Restructuring
	In late 2011, the Company implemented a cost reduction initiative that included workforce reductions and the consolidation of certain facilities.  In total, the Company notified approximately 200 employees of their involuntary termination.  Restructuring activities were completed during the year ended December 30, 2012.
A summary of the pre-tax charges and total costs associated with the initiative is as follows (in thousands):
	Employee Separation costs			Facilities Exit Costs			Other Costs			Total
Amount recorded in accrued liabilities as of January 1, 2012	$	3,496		$	—		$	30		$	3,526
Additional expenses	2,780			221			521			3,522
Cash payments	(6,276		)	(221		)	(551		)	(7,048		)
Amount recorded in accrued liabilities as of December 30, 2012	$	—		$	—		$	—		$	—
Cumulative expense recorded since inception in restructuring expense	$	10,463		$	221		$	974		$	11,658
Accrued Liabilities
Accrued liabilities consist of the following (in thousands):
	December 29,			December 30,
	2013			2012
Accrued compensation expenses	$	82,705		$	59,864
Deferred revenue, current portion	50,834			55,817
Accrued taxes payable	30,435			23,021
Customer deposits	13,569			13,765
Reserve for product warranties	10,407			10,136
Acquisition related contingent consideration liability, current portion	6,719			9,490
Facility exit obligation, current portion	5,570			8,063
Unsettled short-term investment purchase	—			9,154
Other	18,881			12,567
Total accrued liabilities	$	219,120		$	201,877

Acquisitions

Acquisitions	12 Months Ended
	Dec. 29, 2013
Business Combinations [Abstract]	'
Acquisitions	'
	Acquisitions
	Current Year 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. With this acquisition, the Company strengthened its reproductive health product portfolio by gaining access to Verinata’s verifi® non-invasive prenatal test (NIPT) as well as what management believes to be the most comprehensive intellectual property portfolio in the NIPT industry.
	The contractual price for the acquisition was $350.0 million, plus potential cash payments of up to $100.0 million based on the achievement of certain regulatory and revenue milestones. The aggregate purchase price was determined to be $396.3 million, including total cash payment of $339.3 million, $56.2 million in fair value of the contingent milestone payments, $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. In connection with the transaction, the Company deposited into escrow $30.0 million of consideration otherwise payable to shareholders of Verinata. This amount is included in the aggregate consideration and will be held in escrow to cover indemnification claims under the acquisition agreement, if any, for a period of 1.5 years following the completion of the acquisition. As of December 29, 2013, transaction costs of $3.4 million were expensed as incurred in acquisition related (gain) expense, net.
	In conjunction with the acquisition, the Company assumed the Verinata Health, Inc. 2008 Stock Plan and converted, as of the acquisition date, the unvested stock options outstanding under the plan, all of which were in the money, into 0.4 million unvested stock options to purchase Illumina’s common stock, retaining the original vesting schedules. The fair value of all converted options was $18.9 million, $0.2 million of which was attributed to the pre-combination service period and was included in the calculation of purchase price. The remaining fair value will be recognized over the awards’ remaining vesting periods subsequent to the acquisition. The weighted-average acquisition-date fair value of the converted options was determined using the Black-Scholes option pricing model with the following assumptions: (i) market price of $48.36 per share, which was the closing price of Illumina’s common stock on the acquisition date; (ii) weighted average expected term of 2.3 years; (iii) weighted average risk-free interest rate of 0.32%; (iv) weighted average annualized volatility of 42%; and (v) no dividend yield. The weighted average acquisition-date fair value per share of the assumed stock options was $42.63.
	An initial liability of $56.2 million was recorded for an estimate of the acquisition date fair value of the contingent consideration. Any change in the fair value of the contingent milestone consideration subsequent to the acquisition date was and will be recognized in the consolidated statement of income. The fair value of the regulatory milestone payments was measured by the probability-weighted discounted cash flows and the fair value of the revenue milestone payments was measured using a risk-neutral option pricing model, which captures the present value of the expected payment and the probability of reaching the revenue targets. Key assumptions used in the fair value assessments included discount rates ranging from 6% to 20%, volatility of 50%, risk-free rates 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.
	As of December 29, 2013, the allocation of the purchase price to the assets acquired and liabilities assumed on the acquisition date was as follows (in thousands):
		Allocation of purchase price
	Cash and cash equivalents	$	9,151
	Accounts receivable	2,801
	Inventory	1,110
	Prepaid expenses and other current assets	979
	Property and equipment	12,083
	Other assets	978
	Intangible assets	176,490
	Goodwill	227,453
	Accounts payable	(2,539		)
	Accrued liabilities	(3,803		)
	Lease financing obligation	(9,695		)
	Deferred tax liability	(18,741		)
	Total purchase price	$	396,267
	In conjunction with the acquisition, the Company assumed Verinata’s building lease, for which Verinata was considered the accounting owner of the leased building and as such, recorded the fair value of the building as an asset as of the acquisition date. The building is depreciated over a useful life of 30 years. The Company also recorded the related lease financing obligation as a liability assumed, representing the present value of all remaining building lease payments with an interest rate of 6.0%. The annual future minimum payments, including the balloon payment at the end of the lease for the value of the building to be transferred to the landlord, are $0.9 million for each of the years of 2014, 2015, and 2016, and $8.3 million for 2017.
	The following table summarizes the fair value of identifiable intangible assets acquired (amounts in thousands):
		Weighted Average Useful Lives (in years)		Fair Value
	Developed technology	13		$	170,200
	Customer relationships	5		4,690
	Trade name	2		1,600
	Total intangible assets acquired, excluding goodwill			$	176,490
	The fair value of the developed technology and trade name was estimated using an income approach. Under the income approach, an intangible asset’s fair value is equal to the present value of future economic benefits to be derived from ownership of the asset. The estimated fair value was developed by discounting future net cash flows to their present value at market-based rates of return. The fair value of the customer relationships was developed using a cost approach by estimating the time and personnel effort in constructing the customer base. The useful life of the intangible assets for amortization purposes was determined by considering the period of expected cash flows used to measure the fair value of the intangible assets adjusted as appropriate for the entity-specific factors including legal, regulatory, contractual, competitive, economic, or other factors that may limit the useful life of intangible assets.
	The excess of the fair value of the total consideration over the estimated fair value of the net assets was recorded as goodwill, which was primarily attributable to the synergies expected from combining the technologies of Illumina with those of Verinata, including complementary products that will enhance the Company’s overall product portfolio, and the value of the workforce that became our employees following the closing of the acquisitions. The goodwill recognized is not deductible for income tax purposes.
	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 developed technologies of $79.7 million with a weighted average useful life of eight years and goodwill of $126.3 million. 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.
	Pro Forma Information
	The following unaudited pro forma information presents the consolidated results of operations of the Company as if the acquisitions completed during the year ended December 29, 2013 had occurred at the beginning of the applicable annual reporting period, with pro forma adjustments to give effect to intercompany transactions to be eliminated, amortization of intangible assets, share-based compensation, and transaction costs directly associated with the acquisitions (in thousands, except per share amounts):
		Years Ended
		December 29,				December 30,
		2013				2012
	Net revenues	$	1,433,935			$	1,161,241
	Net income	$	113,869			$	92,645
	Net income per share-basic	$	0.91			$	0.75
	Net income per share-diluted	$	0.81			$	0.69
	These unaudited pro forma consolidated financial results have been prepared for illustrative purposes only and do not purport to be indicative of the results of operations that actually would have resulted had the acquisition occurred on the first day of the earliest period presented, or of the future results of the consolidated entities. The unaudited pro forma consolidated financial information does not reflect any operating efficiencies and cost savings that may be realized from the integration of the acquisition.
	Prior Year Acquisitions
	On September 19, 2012, the Company announced the acquisition of BlueGnome Ltd. (BlueGnome), 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.
	The Company estimated the fair value of contingent cash consideration using a probability weighted discounted cash flow approach, a Level 3 measurement, using a discount rate of 30%. The Company also agreed to pay up to $20.0 million to BlueGnome shareholders contingent upon the retention of certain key employees and certain other criteria. Such contingent payments are recognized as contingent compensation expense over the retention period through December 28, 2014.
	As a result of this acquisition, the Company recorded developed technologies of $25.0 million, customer relationships of $16.8 million, and a trade name of $7.1 million with average useful lives of seven, five, and ten years, respectively. The Company recorded the excess consideration of approximately $47.5 million as goodwill.
	On January 10, 2011, the Company acquired Epicentre Technologies Corporation (Epicentre), a provider of nucleic acid sample preparation reagents and specialty enzymes used in sequencing and microarray applications. Total consideration for the acquisition was $71.4 million, which included $59.4 million in net cash payments, $4.6 million in the fair value of contingent consideration settled in stock that is subject to forfeiture if certain non-revenue based milestones are not met, and $7.4 million in the fair value of contingent cash consideration of up to $15.0 million based on the achievement of certain revenue based milestones by January 10, 2013.
	The Company estimated the fair value of contingent stock consideration based on the closing price of its common stock as of the acquisition date. Approximately 229,000 shares of common stock were issued to Epicentre shareholders in connection with the acquisition, which shares are subject to forfeiture if certain non-revenue-based milestones are not met.
	The Company estimated the fair value of contingent cash consideration using a probability weighted discounted cash flow approach, a Level 3 measurement, using a discount rate of 21% and estimated the fair value of contingent stock consideration based on the closing price of its common stock as of the acquisition date. One third of these shares issued with an assessed fair value of $4.6 million were recorded as purchase price and the remaining shares were recorded as compensation costs for post-acquisition service.
	The Company allocated $0.9 million of the total consideration to tangible assets, net of liabilities, and $26.9 million to identified intangible assets, including additional developed technologies of $23.3 million, a trade name of $2.5 million, and customer relationships of $1.1 million, with weighted average useful lives of approximately nine, ten, and three years, respectively. The Company recorded the excess consideration of $43.6 million as goodwill.
	In addition, the Company agreed to pay the former shareholders of another development stage company acquired in 2008 a certain amount of contingent cash consideration based on the achievement of certain product-related and employment-related milestones. In accordance with the applicable accounting guidance effective at the time, such consideration was accounted for as additional elements of the cost of acquisition, resulting in additional IPR&D charges in the years ended January 1, 2012 and January 2, 2011 when the contingencies were resolved beyond a reasonable doubt and the considerations were issued or became issuable.
	Summary of Contingent Compensation Expenses and IPR&D Charges
	Contingent compensation expenses and IPR&D charges as a result of acquisitions consist of the following (in thousands):
		Years Ended
		December 29,				December 30,		January 1,
		2013				2012		2012
	Contingent compensation expense, included in research and development expense	$	544			$	3,419	$	4,799
	Contingent compensation expense, included in selling, general and administrative expense	13,066				5,732		1,258
	Total contingent compensation expense	$	13,610			$	9,151	$	6,057
	IPR&D, included in acquisition related expense (gain), net	$	—			$	—	$	5,425

Intangible_Assets

Intangible Assets	12 Months Ended
	Dec. 29, 2013
Intangible Assets, Net (Excluding Goodwill) [Abstract]	'
Intangible Assets	'
	Intangible Assets
	The Company’s intangible assets, excluding goodwill, include acquired core and licensed technologies, license agreements, trade name, and customer relationships. Amortization for the intangible assets that have finite useful lives is generally recorded on a straight-line basis over their useful lives.
	The following is a summary of the Company’s identifiable intangible assets as of the respective balance sheet dates (in thousands):
		December 29, 2013									December 30, 2012
		Gross				Accumulated			Intangibles,		Gross		Accumulated			Intangibles,
		Carrying				Amortization			Net		Carrying		Amortization			Net
		Amount									Amount
	Licensed technologies	$	48,361			$	(31,927	)	$	16,434	$	47,329	$	(25,471	)	$	21,858
	Core technologies	321,700				(45,534		)	276,166		99,800		(27,427		)	72,373
	Customer relationships	26,770				(7,376		)	19,394		18,780		(2,214		)	16,566
	License agreements	18,917				(4,947		)	13,970		14,404		(3,933		)	10,471
	Trade name	11,800				(6,591		)	5,209		9,600		(672		)	8,928
	Total intangible assets, net	$	427,548			$	(96,375	)	$	331,173	$	189,913	$	(59,717	)	$	130,196
	Additions to intangible assets during the year ended December 29, 2013 were primarily due to acquisitions during the year. The components of such intangibles assets acquired are as follows (in thousands):
		Weighted Average		Gross
		Useful Lives		Carrying
		(years)		Amount
	Core technologies	12		$	249,900
	License agreements	10		10,013
	Customer relationships	4		7,990
	Trade name	2		2,200
	Licensed technologies	5		1,032
	Total intangible asset additions			$	271,135
	The estimated annual amortization of intangible assets for the next five years is shown in the following table (in thousands). Actual amortization expense to be reported in future periods could differ from these estimates as a result of acquisitions, divestitures, asset impairments, among other factors.
		Estimated Annual Amortization
	2014	$	49,376
	2015	45,974
	2016	40,582
	2017	36,106
	2018	27,310
	Thereafter	131,825
	Total	$	331,173

Fair_Value_Measurement

Fair Value Measurement	12 Months Ended
	Dec. 29, 2013
Fair Value Disclosures [Abstract]	'
Fair Value Disclosures	'
	Fair Value Measurements
	The following table presents the Company’s fair value hierarchy for assets and liabilities measured at fair value on a recurring basis as of December 29, 2013 and December 30, 2012, respectively (in thousands):
		December 29, 2013									December 30, 2012
		Level 1			Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
	Assets:
	Money market funds (cash equivalent)	$	478,755		$	—	$	—	$	478,755	$	252,126	$	—	$	—	$	252,126
	Debt securities in government-sponsored entities	—			82,143		—		82,143		—		314,873		—		314,873
	Corporate debt securities	—			341,970		—		341,970		—		472,861		—		472,861
	U.S. Treasury securities	29,853			—		—		29,853		128,489		—		—		128,489
	Deferred compensation plan assets	—			17,805		—		17,805		—		13,626		—		13,626
	Total assets measured at fair value	$	508,608		$	441,918	$	—	$	950,526	$	380,615	$	801,360	$	—	$	1,181,975
	Liabilities:
	Acquisition related contingent consideration liabilities	$	—		$	—	$	49,480	$	49,480	$	—	$	—	$	12,519	$	12,519
	Deferred compensation liability	—			14,957		—		14,957		—		12,071		—		12,071
	Total liabilities measured at fair value	$	—		$	14,957	$	49,480	$	64,437	$	—	$	12,071	$	12,519	$	24,590
	The Company holds available-for-sale securities that consist of highly liquid, investment grade debt securities. The Company determines the fair value of its debt securities based upon one or more valuations reported by its investment accounting and reporting service provider.  The investment service provider values the securities using a hierarchical security pricing model that relies primarily on valuations provided by 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 certain 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.
	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 fair value of the contingent considerations during the years ended December 29, 2013, December 30, 2012, and January 1, 2012 were due to changes in the estimated payments and a shorter discounting period.
	Changes in estimated fair value of contingent consideration liabilities from January 2, 2011 through December 29, 2013 are as follows (in thousands):
		Contingent
		Consideration
		Liability
		(Level 3 Measurement)
	Balance as of January 2, 2011	$	3,738
	Acquisition of Epicentre	7,400
	Change in estimated fair value, recorded in acquisition related (gain) expense, net	(4,500		)
	Balance as of January 1, 2012	6,638
	Acquisition of BlueGnome	7,500
	Change in estimated fair value, recorded in acquisition related (gain) expense, net	1,975
	Cash payments	(3,594		)
	Balance as of December 30, 2012	12,519
	Additional liability recorded for current period acquisitions	60,184
	Change in estimated fair value, recorded in acquisition related (gain) expense, net	(18,784		)
	Cash payments	(4,439		)
	Balance as of December 29, 2013	$	49,480

Convertible_Senior_Notes

Convertible Senior Notes	12 Months Ended
	Dec. 29, 2013
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) in an offering conducted in accordance with Rule 144A under the Securities Act of 1933, as amended. The 2016 Notes were issued at 98.25% of par value. Debt issuance costs of approximately $0.4 million were primarily comprised of legal, accounting, and other professional fees, the majority of which were recorded in other noncurrent assets and are being amortized to interest expense over the five-year term of the 2016 Notes.
	The 2016 Notes will be convertible into cash, shares of common stock, or a combination of cash and shares of common stock, at the Company’s election, based on an initial conversion rate, subject to adjustment, of 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.
	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. In general, for each $1,000 in principal, the “principal portion” of cash upon settlement is defined as the lesser of $1,000, and the conversion value during the 20-day observation period as described in the indenture for the 2016 Notes. The conversion value is the sum of the daily conversion value which is the product of the effective conversion rate divided by 20 days and the daily volume weighted average price (“VWAP”) of the Company’s common stock. The “share amount” is the cumulative “daily share amount” during the observation period, which is calculated by dividing the daily VWAP into the difference between the daily conversion value (i.e., conversion rate x daily VWAP) and $1,000.
	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. If a designated event, as defined in the indenture for the 2016 Notes, such as an acquisition, merger, or liquidation, occurs prior to the maturity date, subject to certain limitations, holders of the 2016 Notes may require the Company to repurchase all or a portion of their 2016 Notes for cash at a repurchase price equal to 100% of the principal amount of the 2016 Notes to be repurchased, plus any accrued and unpaid interest to, but excluding, the repurchase date.
	The Company accounts separately for the liability and equity components of the 2016 Notes in accordance with authoritative guidance for convertible debt instruments that may be settled in cash upon conversion. The guidance requires the carrying amount of the liability component to be estimated by measuring the fair value of a similar liability that does not have an associated conversion feature. Because the Company has no outstanding non-convertible public debt, the Company determined that senior, unsecured corporate bonds traded on the market represent a similar liability to the convertible senior notes without the conversion option. Based on market data available for publicly traded, senior, unsecured corporate bonds issued by companies in the same industry and with similar maturity, the Company estimated the implied interest rate of its 2016 Notes to be 4.5%, assuming no conversion option. Assumptions used in the estimate represent what market participants would use in pricing the liability component, including market interest rates, credit standing, and yield curves, all of which are defined as Level 2 observable inputs. The estimated implied interest rate was applied to the 2016 Notes, which resulted in a fair value of the liability component of $748.5 million upon issuance, calculated as the present value of implied future payments based on the $920.0 million aggregate principal amount. The $155.4 million difference between the cash proceeds of $903.9 million and the estimated fair value of the liability component was recorded in additional paid-in capital as the 2016 Notes were not considered redeemable.
	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 dilutive impact of the 2016 Notes. During the years ended December 29, 2013 and December 30, 2012, the 2016 Notes were not convertible. However, as the market price of the Company’s common stock exceeded the conversion price during the last months of 2013, the calculation of dilutive potential common shares outstanding for the year ended December 29, 2013 reflects the dilutive impact from the 2016 Notes. The 2016 Notes had no dilutive impact for the year ended December 30, 2012. If the 2016 Notes were converted as of December 29, 2013, the if-converted value would exceed the principal amount by $209.0 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). The Company pays 0.625% interest per annum on the principal amount of the 2014 Notes semi-annually in arrears in cash on February 15 and August 15 of each year. The 2014 Notes mature on February 15, 2014. The effective interest rate of the liability component was estimated to be 8.3%.
	The Company entered into hedge transactions concurrently with the issuance of the 2014 Notes under which the Company is entitled to purchase up to approximately 18.3 million shares of the Company’s common stock at a strike price of approximately $21.83 per share, subject to adjustment. The convertible note hedge transactions had the effect of reducing dilution to the Company’s stockholders upon conversion of the 2014 Notes. Also concurrently with the issuance of the 2014 Notes, the Company sold to the hedge counterparties warrants exercisable, on a cashless basis, for up to approximately 18.3 million shares of the Company’s common stock at a strike price of $31.435 per share, subject to adjustment. The proceeds from these warrants partially offset the cost to the Company of the convertible note hedge transactions.
	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. In all cases of conversions of the 2014 Notes, the principal amount of all 2014 Notes 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 such conversion. As of December 29, 2013, there remained in place the balance of the convertible note hedge transactions with respect to $29.6 million principal amount of the 2014 Notes, which are convertible for up to approximately 1.4 million shares of the Company’s common stock. If the remaining 2014 Notes were converted as of December 29, 2013, the if-converted value would exceed the principal amount by $109.3 million.
	As a result of the conversions during the year ended December 29, 2013, the Company recorded 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 as in the issuance date valuation.
	The following table summarizes information about the conversion of the 2014 Notes during year ended December 29, 2013 (in thousands, except percentages):
			2014 Notes
	Cash paid for principal of notes converted		$	10,555
	Conversion value over principal amount paid in shares of common stock		$	21,217
	Number of shares of common stock issued upon conversion		317
	Loss on extinguishment of debt		$	555
	Effective interest rate used to measure fair value of converted notes upon conversion		0.5% - 0.8%
	The following table summarizes information about the equity and liability components of the 2014 and 2016 Notes (dollars in thousands). The fair values of the respective notes outstanding were measured based on quoted market prices.
		December 29, 2013			December 30, 2012
	Principal amount of convertible notes outstanding	$	949,570		$	960,125
	Unamortized discount of liability component	(80,977		)	(117,752		)
	Net carrying amount of liability component	868,593			842,373
	Less: current portion	(29,288		)	(36,967		)
	Long-term debt	$	839,305		$	805,406
	Conversion option subject to cash settlement	$	282		$	3,158
	Carrying value of equity component, net of issuance costs	$	274,304		$	271,966
	Fair value of outstanding notes	$	1,428,743		$	993,916
	Weighted average remaining amortization period of discount on the liability component	2 years			3 years

Commitments

Commitments	12 Months Ended
	Dec. 29, 2013
Commitments and Contingencies Disclosure [Abstract]	'
Commitments	'
	Commitments
	Leases
	The Company leases office and manufacturing facilities under various noncancellable lease agreements. Facility leases generally provide for periodic rent increases, and many contain escalation clauses and renewal options. Certain leases require the Company to pay property taxes and routine maintenance. The Company is headquartered in San Diego, California and leases facilities in San Diego and the San Francisco Bay Area in California; Madison, Wisconsin; Morrisville, North Carolina; Australia; Brazil; China; France; Japan; Singapore; the Netherlands; and the United Kingdom. The lease for the Company’s headquarters expires in 2031, with four five-year options to extend.
	During 2013, the Company entered into an agreement to sublease sections of its former headquarters. The sublease has an initial term of approximately ten years. In conjunction with the sublease, the Company issued a letter of credit in the amount of $8.0 million, which will decrease ratably to zero over the term of the sublease.
	Annual future minimum payments under operating leases as of December 29, 2013 were as follows (in thousands):
		Operating Leases			Sublease Income			Net Operating Leases
	2014	$	29,526		$	(2,478	)	$	27,048
	2015	29,463			(2,552		)	26,911
	2016	29,327			(2,629		)	26,698
	2017	29,383			(2,708		)	26,675
	2018	29,601			(2,789		)	26,812
	Thereafter	395,342			(14,708		)	380,634
	Total minimum lease payments	$	542,642		$	(27,864	)	$	514,778
	Rent expenses were $28.1 million, $21.4 million, and $17.4 million for the years ended December 29, 2013, December 30, 2012, and January 1, 2012, respectively.
	The Company recorded facility exit obligations upon vacating its former headquarters during the years ended December 29, 2013, December 30, 2012, and January 1, 2012. Changes in the facility exit obligation from January 1, 2012 through December 29, 2013 are as follows (in thousands):
		Headquarter Facility Exit Obligation
	Balance as of January 1, 2012:	$	25,049
	Adjustment to facility exit obligation	24,878
	Accretion of interest expense	2,129
	Cash payments	(6,704		)
	Balance as of December 30, 2012:	45,352
	Adjustment to facility exit obligation	(114		)
	Accretion of interest expense	2,738
	Cash payments	(9,758		)
	Balance as of December 29, 2013	$	38,218
	Warranties
	Changes in the Company’s reserve for product warranties from January 2, 2011 through December 29, 2013 are as follows (in thousands):
		Warranty Reserve
	Balance as of January 2, 2011	$	16,761
	Additions charged to cost of revenue	17,913
	Repairs and replacements	(22,708		)
	Balance as of January 1, 2012	11,966
	Additions charged to cost of revenue	17,279
	Repairs and replacements	(19,109		)
	Balance as of December 30, 2012	10,136
	Additions charged to cost of revenue	15,674
	Repairs and replacements	(15,403		)
	Balance as of December 29, 2013	$	10,407

Sharebased_Compensation_Expens

Share-based Compensation Expense	12 Months Ended
	Dec. 29, 2013
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Share-based Compensation Expense	'
	Share-based Compensation Expense
	Total share-based compensation expense for all stock awards consists of the following (in thousands):
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	Cost of product revenue	$	6,223		$	7,575		$	6,951
	Cost of service and other revenue	777			461			695
	Research and development	37,439			30,879			32,105
	Selling, general and administrative	61,387			55,409			52,341
	Share-based compensation expense before taxes	105,826			94,324			92,092
	Related income tax benefits	(32,819		)	(30,759		)	(32,168		)
	Share-based compensation expense, net of taxes	$	73,007		$	63,565		$	59,924
	The assumptions used for the specified reporting periods and the resulting estimates of weighted-average fair value per share of options granted and for stock purchased under the ESPP during those periods are as follows:
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	Stock options granted:
	Risk-free interest rate	0.14 - 1.86%			0.56 - 0.93%			0.85 - 2.23%
	Expected volatility	30 - 44%			41 - 48%			41 - 53%
	Expected term	0.8 - 9.4 years			4.0 - 6.6 years			4.7 - 5.5 years
	Expected dividends	—			—			—
	Weighted average fair value per share	$	40.66		$	15.47		$	27.47
	Stock purchased under the ESPP:
	Risk-free interest rate	0.08 - 0.15%			0.09 - 0.17%			0.16 - 0.30%
	Expected volatility	31 - 32%			33 - 64%			43 - 48%
	Expected term	0.5 - 1.0 year			0.5 - 1.0 year			0.5 - 1.0 year
	Expected dividends	—			—			—
	Weighted average fair value per share	$	19.3		$	16.45		$	20.08
	As of December 29, 2013, approximately $216.9 million of total unrecognized compensation cost related to stock options, restricted stock, and ESPP shares issued to date is expected to be recognized over a weighted-average period of approximately 2.2 years.

Stockholders_Equity

Stockholders' Equity	12 Months Ended
	Dec. 29, 2013
Equity [Abstract]	'
Stockholders' Equity	'
	Stockholders’ Equity
	The Company’s 2005 Stock and Incentive Plan (the 2005 Stock Plan), 2005 Solexa Equity Incentive Plan (the 2005 Solexa Equity Plan), the Verinata Health, Inc. 2008 Stock Plan (the 2008 Stock Plan), and the New Hire Stock and Incentive Plan allow for the issuance of stock options, restricted stock units and awards, and performance stock units. During December 29, 2013, the stockholders ratified an amendment to increase the maximum number of shares of common stock authorized for issuance under the 2005 Stock Plan by 5.0 million shares. As of December 29, 2013, approximately 6.8 million shares remained available for future grants under the 2005 Stock Plan, the 2005 Solexa Equity Plan, and the 2008 Verinata Health Stock Plan. There is no set number of shares reserved for issuance under the New Hire Stock and Incentive Plan.
	Stock Options
	Stock options granted at the time of hire primarily vest over a four or five-year period, with 25% or 20% of options vesting on the first anniversary of the grant date and the remaining options vesting monthly over the remaining vesting period. Stock options granted subsequent to hiring primarily vest monthly over a four or five-year period. Each grant of options has a maximum term of ten years, measured from the applicable grant date, subject to earlier termination if the optionee’s service ceases. Vesting in all cases is subject to the individual’s continued service through the vesting date. The Company satisfies option exercises through the issuance of new shares.
	The Company’s stock option activity under all stock option plans from January 2, 2011 through December 29, 2013 is as follows:
		Options		Weighted-
		(in thousands)		Average
				Exercise Price
	Outstanding at January 2, 2011	11,882		$	22.83
	Granted	1,399		64.98
	Exercised	(2,784	)	17.98
	Cancelled	(119	)	33.49
	Outstanding at January 1, 2012	10,378		29.69
	Granted	251		40.79
	Exercised	(2,071	)	20.34
	Cancelled	(207	)	39.18
	Outstanding at December 30, 2012	8,351		32.1
	Granted	512		14.74
	Exercised	(3,006	)	27.7
	Cancelled	(133	)	41.8
	Outstanding at December 29, 2013	5,724		$	32.64
	At December 29, 2013, outstanding options to purchase 4.7 million shares were exercisable with a weighted average per share exercise price of $31.83. The weighted average remaining life of options outstanding and exercisable is 4.9 years and 4.5 years, respectively, as of December 29, 2013.
	The aggregate intrinsic value of options outstanding and options exercisable as of December 29, 2013 was $445.0 million and $370.9 million, respectively. Aggregate intrinsic value represents the product of the number of options outstanding multiplied by the difference between the Company’s closing stock price per share on the last trading day of the fiscal period, which was $110.38 as of December 27, 2013, and the exercise price. Total intrinsic value of options exercised was $141.7 million, $60.6 million, and $136.5 million for the years ended December 29, 2013, December 30, 2012, and January 1, 2012, respectively. Total fair value of options vested was $24.0 million, $31.9 million, and $49.5 million for the years ended December 29, 2013, December 30, 2012, and January 1, 2012, respectively.
	Restricted Stock
	The Company issues restricted stock units (RSU), restricted stock awards (RSA), and performance stock units (PSU). The Company grants RSU and PSU pursuant to its 2005 Stock and Incentive Plan and 2008 Stock Plan. RSU are share awards that, upon vesting, will deliver to the holder shares of the Company’s common stock. For grants to new hires prior to July 2011 and for grants to existing employees, RSU generally vest 15% on the first anniversary of the grant date, 20% on the second anniversary of the grant date, 30% on the third anniversary of the grant date, and 35% on the fourth anniversary of the grant date. For grants to new hires subsequent to July 2011, RSU generally vest over a four-year period with equal vesting on anniversaries of the grant date. The Company satisfies RSU vesting through the issuance of new shares. The Company issues PSU for which the number of shares issuable at the end of a three-year performance period will range from 50% and 150% of the shares approved in the award based on the Company’s performance relative to specified earnings per share targets.
	The Company also issues RSA that are released based on service related vesting conditions. RSA may be issued from the Company’s treasury stock or granted pursuant to the Company’s 2005 Stock and Incentive Plan.
	A summary of the Company’s restricted stock activity and related information from January 2, 2011 through December 29, 2013 is as follows (in thousands, except per share amounts):
										Weighted Average
										Grant-Date Fair Value per Share
		RSA		RSU			PSU			RSA		RSU		PSU
	Outstanding at January 2, 2011	—		3,109			—			$	—	$	40.39	$	—
	Awarded	230		1,550			—			65.95		42.02		—
	Vested	—		(827	)		—			—		36.47		—
	Cancelled	—		(356	)		—			—		42.15		—
	Outstanding at January 1, 2012	230		3,476			—			65.95		41.87		—
	Awarded	312		1,640			599			47.91		48.52		49.66
	Vested	(77	)	(1,062	)		—			65.95		38.48		—
	Cancelled	—		(394	)		(12	)		—		45.05		50.54
	Outstanding at December 30, 2012	465		3,660			587			53.84		45.49		49.64
	Awarded	—		1,532			584			—		77.53		59.16
	Vested	(217	)	(1,308	)		—			54.27		42.97		—
	Cancelled	—		(256	)		(70	)		—		49.24		50.42
	Outstanding at December 29, 2013	248		3,628			1,101			$	53.46	$	59.66	$	54.64
	Pre-tax intrinsic values of all outstanding restricted and performance stock and total fair values of vested restricted and performance stock are as follows (in thousands):
		Years Ended
		December 29,			December 30,				January 1,
		2013			2012				2012
	Pre-tax intrinsic value of outstanding restricted and performance stock:
	RSA	$	27,384		$	25,437			$	6,986
	RSU	400,421			200,383				105,944
	PSU	121,555			32,149				—
	Fair value of restricted and performance stock vested:
	RSA	$	11,750		$	5,039			—
	RSU	56,212			40,870				30,155
	PSU	—			—				—
	Employee Stock Purchase Plan
	A total of 15.5 million shares of the Company’s common stock have been reserved for issuance under its 2000 Employee Stock Purchase Plan, or ESPP. The ESPP permits eligible employees to purchase common stock at a discount, but only through payroll deductions, during defined offering periods. The price at which stock is purchased under the 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. The initial offering period commenced in July 2000.
	The ESPP provides for annual increases of shares available for issuance by the lesser of 3% of the number of outstanding shares of the Company’s common stock on the last day of the immediately preceding fiscal year, 3.0 million shares, or such lesser amount as determined by the Company’s board of directors. Approximately 400,000, 328,000, and 328,000 shares were issued under the ESPP during the years ended December 29, 2013, December 30, 2012, and January 1, 2012, respectively. As of December 29, 2013 and December 30, 2012, there were approximately 15.0 million and 15.4 million shares available for issuance under the ESPP, respectively.
	Warrants
	In connection with the offering of the Company’s 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. 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 December 29, 2013, warrants to purchase 15.4 million shares of the Company’s common stock remained outstanding. All outstanding warrants expire in equal installments during the 40 consecutive scheduled trading days beginning on May 16, 2014.
	During the year ended January 1, 2012, the remaining warrants assumed by the Company in a prior acquisition to purchase approximately 505,000 shares of the Company’s common stock were exercised, resulting in cash proceeds to the Company of approximately $5.5 million.
	Share Repurchases
	During the years ended December 29, 2013, December 30, 2012, and January 1, 2012, the Company repurchased approximately 0.9 million shares for $50.0 million, 1.9 million shares for $82.5 million, and 2.4 million shares for $156.0 million, respectively. In addition, concurrently with the issuance of the Company’s 2016 Notes in 2011, approximately 4.9 million shares were repurchased for $314.3 million.
As of December 29, 2013, the Company had authorization to repurchase up to an additional $117.5 million of its common stock, which was part of the $250.0 million stock repurchase program authorized by the Board of Directors in April 2012 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.
In August 2011, the Company’s board of directors authorized a $100.0 million discretionary repurchase program, which became completely utilized as of January 1, 2012. In July 2010, the Company’s board of directors authorized a $200.0 million stock repurchase program, with $100.0 million allocated to repurchasing Company common stock under a 10b5-1 plan over a twelve month period and $100.0 million allocated to repurchasing Company common stock at management’s discretion during open trading windows. This authorized repurchase amount had been utilized completely as of January 1, 2012.
Stockholder Rights Plan
In connection with the unsolicited tender offer by Roche (refer to note “15. Unsolicited Tender Offer”), on January 25, 2012, the Company’s Board of Directors declared a dividend of one preferred share purchase right (Right) for each outstanding share of the Company’s common stock. Each Right entitled the registered holder to purchase from the Company one one-thousandth of a share of the Company’s Series A Junior Participating Preferred Stock, par value $0.01 per share (Preferred Shares), at a price of $275.00 per one thousandth of a Preferred Share, subject to adjustment. The Rights were not exercisable until such time that the Board of Directors determined to eliminate its deferral of the date on which separate Rights certificates are issued and the Rights traded separately from the Company’s common stock (Distribution Date). If a person or group (triggering party) acquired 15% or more of the Company’s outstanding common stock, each Right would have entitled holders other than the triggering party to purchase, at the exercise price of the Right, a number of shares of common stock having a market value of two times the exercise price of the Right. If the Company was acquired in a merger or other business combination transaction after a person acquires 15% or more of the Company’s common stock, each Right would have entitled holders other than the triggering party to purchase, at the Right’s then-current exercise price, a number of common shares of the acquiring company that at the time of such transaction have a market value of two times the exercise price of the Right. The Board of Directors would have been entitled to redeem the Rights at a price of $0.001 per Right at any time before the Distribution Date. The Board of Directors would have been entitled to exchange the Rights at an exchange ratio per Right of one share of common stock after any person acquires beneficial ownership of 15% or more of the Company’s outstanding common stock, and prior to the acquisition of 50% or more of the Company’s outstanding common stock. In 2013, the expiration date was amended to March 27, 2013 from January 26, 2017, and the Rights expired accordingly.

Legal_Proceedings

Legal Proceedings	12 Months Ended
	Dec. 29, 2013
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. In November and December 2012, the Company filed motions for summary judgment that the patent is not infringed and is invalid, and that Syntrix’s trade secrets claims are barred by various statutes of limitation. Syntrix filed a motion for summary judgment that the patent is valid. 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. The Court denied Syntrix’s motion for summary judgment on validity, and denied the Company’s motion for summary judgment for non-infringement and invalidity. 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. On July 17, 2013, the Company filed a post-trial motion asking the District Court to vacate the amended judgment and enter judgment as a matter of law in the Company’s favor or, alternatively, to grant a new trial. On November 4, 2013, the Court issued an Order denying the Company’s motion for judgment as a matter of law and upholding the jury verdict. 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.
	As a result of the amended judgment, the Company has recorded a legal contingency accrual of $132.9 million as of December 29, 2013, which includes the damages and prejudgment interest awarded to Syntrix, estimated additional damages through December 29, 2013, and an estimate of interest accrued on the damages subsequent to June 19, 2013. For the year ended December 29, 2013, such charges totaled $132.9 million, $114.6 million of which was recorded within operating expenses, and the remainder was recorded to cost of sales. In December 2013, the Company secured the amount of the judgment by executing a supersedeas bond and deposited $12.0 million of the accrued post-judgment ongoing royalty amounts with the Court. 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.

Income_Taxes

Income Taxes	12 Months Ended
	Dec. 29, 2013
Income Tax Disclosure [Abstract]	'
Income Tax Disclosure [Text Block]	'
	Income Taxes
	The income (loss) before income taxes summarized by region is as follows (in thousands):
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	United States	$	(53,703	)	$	102,296		$	(7,100	)
	Foreign	213,017			120,312			140,145
	Total income before income taxes	$	159,314		$	222,608		$	133,045
	The provision for income taxes consists of the following (in thousands):
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	Current:
	Federal	$	78,419		$	57,285		$	43,161
	State	8,854			10,121			3,958
	Foreign	39,416			31,504			24,154
	Total current provision	126,689			98,910			71,273
	Deferred:
	Federal	(69,102		)	(7,724		)	(22,738		)
	State	(15,222		)	(7,708		)	(8,050		)
	Foreign	(8,359		)	(12,124		)	5,932
	Total deferred benefit	(92,683		)	(27,556		)	(24,856		)
	Total tax provision	$	34,006		$	71,354		$	46,417
	The provision for income taxes reconciles to the amount computed by applying the federal statutory rate to income before taxes as follows (in thousands):
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	Tax at federal statutory rate	$	55,760		$	77,913		$	46,566
	State, net of federal benefit	647			4,056			(49		)
	Research and other credits	(10,977		)	(2,613		)	(7,418		)
	Acquired in-process research & development	—			137			1,989
	Change in valuation allowance	10,544			(37		)	(688		)
	Permanent differences	1,120			2,380			1,668
	Change in fair value of contingent consideration	(3,859		)	—			(1,311		)
	Impact of foreign operations	(18,006		)	(11,470		)	5,579
	Other	(1,223		)	988			81
	Total tax provision	$	34,006		$	71,354		$	46,417
	Significant components of the Company’s deferred tax assets and liabilities are as follows (in thousands):
		December 29,			December 30,
		2013			2012
	Deferred tax assets:
	Net operating losses	$	66,969		$	2,564
	Tax credits	36,277			16,447
	Other accruals and reserves	103,539			47,306
	Stock compensation	36,728			39,175
	Inventory adjustments	9,034			8,977
	Impairment of cost-method investment	3,540			1,406
	Other amortization	9,571			5,195
	Other	14,704			13,469
	Total gross deferred tax assets	280,362			134,539
	Valuation allowance on deferred tax assets	(19,132		)	(1,756		)
	Total deferred tax assets	261,230			132,783
	Deferred tax liabilities:
	Purchased intangible amortization	(98,671		)	(20,116		)
	Convertible debt	(27,821		)	(38,910		)
	Property and equipment	(13,311		)	(10,867		)
	Other	(6,349		)	(6,682		)
	Total deferred tax liabilities	(146,152		)	(76,575		)
	Net deferred tax assets	$	115,078		$	56,208
	A valuation allowance is established when it is more likely than not the future realization of all or some of the deferred tax assets will not be achieved. The evaluation of the need for a valuation allowance is performed on a jurisdiction-by-jurisdiction basis, and includes a review of all available positive and negative evidence. Based on the available evidence as of December 29, 2013, the Company was not able to conclude it is more likely than not certain U.S. deferred tax assets will be realized. Therefore, the Company recorded a valuation allowance of $19.1 million against certain U.S. deferred tax assets. During the year ended December 29, 2013, the valuation allowance increased by $17.4 million, primarily due to a $10.5 million increase in the provision for income taxes as a result of the estimated limitation on foreign tax credit utilization in the United States, and a $6.8 million increase in goodwill related to pre-acquisition deferred tax assets from entities acquired during the year.
	As of December 29, 2013, the Company had net operating loss carryforwards for federal and state tax purposes of $164.2 million and $228.1 million, respectively, which will begin to expire in 2020 and 2014, respectively, unless utilized prior. In addition, the Company also had federal and state tax credit carryforwards of $16.1 million and $51.5 million, respectively, which will begin to expire in 2023 and 2019, respectively, unless utilized prior.
	Pursuant to Section 382 and 383 of the Internal Revenue Code, utilization of the Company’s net operating loss and credits may be subject to annual limitations in the event of any significant future changes in its ownership structure. These annual limitations may result in the expiration of net operating losses and credits prior to utilization. The deferred tax assets as of December 29, 2013 are net of any previous limitations due to Section 382 and 383.
	The Company recognizes excess tax benefits associated with share-based compensation to stockholders’ equity only when realized. When assessing whether excess tax benefits relating to share-based compensation have been realized, the Company follows the with-and-without approach excluding any indirect effects of the excess tax deductions. Under this approach, excess tax benefits related to share-based compensation are not deemed to be realized until after the utilization of all other tax benefits available to the Company. During the year ended December 29, 2013, the Company realized $53.0 million of such excess tax benefits, and recorded a corresponding credit to additional paid in capital. As of December 29, 2013, the Company has $3.6 million of unrealized excess tax benefits associated with share-based compensation. These tax benefits will be accounted for as a credit to additional paid-in capital, if and when realized, rather than a reduction of the provision for income taxes.
The Company’s manufacturing operations in Singapore operate under various tax holidays and incentives that will expire in 2018. For the year ended December 29, 2013, these tax holidays and incentives resulted in a $7.5 million decrease to the provision for income taxes and an increase in net income per diluted share of $0.05.
It is the Company’s intention to indefinitely reinvest all current and future foreign earnings in order to ensure sufficient working capital to support and expand existing operations outside the United States. Accordingly, residual U.S. income taxes have not been provided on $235.1 million of undistributed earnings of foreign subsidiaries as of December 29, 2013. In the event the Company was required to repatriate funds from outside of the United States, such repatriation would be subject to local laws, customs, and tax consequences.
The following table summarizes the gross amount of the Company’s uncertain tax positions (in thousands):
	December 29,			December 30,			January 1,
	2013			2012			2012
Balance at beginning of year	$	37,585		$	28,396		$	22,729
Increases related to prior year tax positions	4,794			2,573			875
Decreases related to prior year tax positions	(223		)	(69		)	(382		)
Increases related to current year tax positions	7,503			6,685			5,174
Decreases related to lapse of statute of limitations	(613		)	—			—
Balance at end of year	$	49,046		$	37,585		$	28,396
Included in the balance of uncertain tax positions as of December 29, 2013, and December 30, 2012, are $40.1 million and $29.9 million, respectively, of net unrecognized tax benefits that, if recognized, would reduce the Company’s effective income tax rate in future periods.
Any interest and penalties related to uncertain tax positions are reflected in the provision for income taxes. The Company recognized expense of $1.0 million, $0.8 million, and $1.1 million, related to potential interest penalties on uncertain tax positions during the years ended December 29, 2013, December 30, 2012, and January 1, 2012, respectively. The Company recorded a liability for potential interest and penalties of $3.5 million and $2.1 million as of December 29, 2013 and December 30, 2012, respectively.
The Company is currently under examination by the IRS for tax year 2011. The IRS continues to gather information regarding the 2011 federal tax return and has not yet proposed any adjustments to the filed return. Tax years 1997 to 2013 remain subject to future examination by the major tax jurisdictions in which the Company is subject to tax. Given the uncertainty of potential adjustments from the current examination as well as the impact of the current examination on the potential expiration of the statute of limitations, it is reasonably possible that the balance of unrecognized tax benefits could change significantly over the next 12 months. However, at this time, an estimate of the range of reasonably possible adjustments to the balance of unrecognized tax benefits cannot be determined given the number of matters being examined and the number of years that are potentially subject to examination.

Employee_Benefit_Plans

Employee Benefit Plans	12 Months Ended
	Dec. 29, 2013
Postemployment Benefits [Abstract]	'
Employee Benefit Plans	'
	Employee Benefit Plans
	Retirement Plan
	The Company has a 401(k) savings plan covering substantially all of its employees in the United States. Company contributions to the plan are discretionary. During the years ended December 29, 2013, December 30, 2012, and January 1, 2012, the Company made matching contributions of $7.0 million, $5.5 million, and $5.3 million, respectively.
	Deferred Compensation Plan
	The Company adopted the Illumina, Inc. Deferred Compensation Plan (the Plan) that became effective January 1, 2008. Eligible participants, which include the Company’s senior level employees and members of the board of directors, can contribute up to 80% of their base salary and 100% of all other forms of compensation into the Plan, including bonus, equity awards, commission, and director fees. The Company has agreed to credit the participants’ contributions with earnings that reflect the performance of certain independent investment funds. On a discretionary basis, the Company may also make employer contributions to participant accounts in any amount determined by the Company. The vesting schedules of employer contributions are at the sole discretion of the Compensation Committee. However, all employer contributions shall become 100% vested upon the occurrence of the participant’s disability, death or retirement or a change in control of the Company. The benefits under this plan are unsecured. Participants are generally eligible to receive payment of their vested benefit at the end of their elected deferral period or after termination of their employment with the Company for any reason or at a later date to comply with the restrictions of Section 409A. As of December 29, 2013, no employer contributions were made to the Plan.
	In January 2008, the Company also established a rabbi trust for the benefit of the participants under the Plan. In accordance with authoritative guidance related to consolidation of variable interest entities and accounting for deferred compensation arrangements where amounts earned are held in a rabbi trust and invested, the Company has included the assets of the rabbi trust in its consolidated balance sheet since the trust’s inception. As of December 29, 2013 and December 30, 2012, the assets of the trust were $17.8 million and $13.6 million, respectively, and liabilities of the Company were $15.0 million and $12.1 million, respectively. The assets and liabilities are classified as other assets and accrued liabilities, respectively, on the Company’s consolidated balance sheets. Changes in the values of the assets held by the rabbi trust are recorded in other (expense) income, net in the consolidated statement of income, and changes in the values of the deferred compensation liabilities are recorded in cost of sales or operating expenses.

Segment_Information_Geographic

Segment Information, Geographic Data, and Significant Customers	12 Months Ended
	Dec. 29, 2013
Segment Reporting [Abstract]	'
Segment Information, Geographic Data, and Significant Customers	'
	Segment Information, Geographic Data, and Significant Customers
	For 2013 and prior, the Company was organized in two operating segments: Life Sciences and Diagnostics. Life Sciences operating segment included all products and services related to the research market, namely the product lines based on the Company’s sequencing, BeadArray, and real-time PCR technologies. The Diagnostics operating segment focused on opportunities in molecular diagnostics. During all periods presented, the Diagnostics operating segment had limited activity. Accordingly, the Company’s operating results for both units were reported on an aggregate basis as one reportable segment.
	In late 2013, we announced organizational changes effective December 30, 2013, for the primary purpose of achieving scalability in our business operations to support our growth in strategic markets. The Company has separated the roles of the Chief Executive Officer and the President, with core market and operational groups reporting to the President, and corporate functions and the President reporting to the CEO. As a result, the Company began operations as one operating segment starting in December 30, 2013, and will continue to report under one reportable segment.
	The Company had revenue in the following regions for the years ended December 29, 2013, December 30, 2012, and January 1, 2012 (in thousands):
		Years Ended
		December 29,		December 30,		January 1,
		2013		2012		2012
	United States	$	714,662	$	568,443	$	528,723
	Europe	354,682		291,404		277,971
	Asia-Pacific	276,442		232,498		197,005
	Other markets	75,392		56,171		51,836
	Total	$	1,421,178	$	1,148,516	$	1,055,535
	Revenues are attributable to geographic areas based on the region of destination.
	The majority of our product sales consist of consumables and instruments. For the years ended December 29, 2013, December 30, 2012, and January 1, 2012, consumable sales represented 62%, 64%, and 56%, respectively, of total revenues and instrument sales comprised 26%, 27%, and 35%, respectively, of total revenues. The Company’s customers include leading genomic research centers, academic institutions, government laboratories, hospitals, and reference laboratories, as well as pharmaceutical, biotechnology, agrigenomics, commercial molecular diagnostic, and consumer genomics companies. The Company had no customers that provided more than 10% of total revenue in the years ended December 29, 2013, December 30, 2012, and January 1, 2012.
	Net long-lived assets exclude goodwill and other intangible assets since they are not allocated on a geographic basis. The Company had net long-lived assets consisting of property and equipment in the following regions as of December 29, 2013 and December 30, 2012 (in thousands):
		December 29,		December 30,
		2013		2012
	United States	$	150,470	$	126,749
	United Kingdom	24,122		21,740
	Singapore	21,311		12,504
	Other countries	6,763		5,174
	Total	$	202,666	$	166,167

Quarterly_Financial_Informatio

Quarterly Financial Information (unaudited)	12 Months Ended
	Dec. 29, 2013
Quarterly Financial Information Disclosure [Abstract]	'
Quarterly Financial Information (unaudited)	'
	Quarterly Financial Information (unaudited)
	The following financial information reflects all normal recurring adjustments, which are, in the opinion of management, necessary for a fair statement of the results and cash flows of interim periods. All quarters for fiscal years 2013 and 2012 ended December 29, 2013 and December 30, 2012 were 13 weeks. Summarized quarterly data for fiscal years 2013 and 2012 are as follows (in thousands except per share data):
		First Quarter			Second Quarter		Third Quarter		Fourth Quarter
	2013
	Total revenue	$	330,958		$	346,094	$	356,800	$	387,326
	Gross profit	$	219,292		$	223,409	$	209,940	$	259,246
	Net (loss) income	$	(22,587	)	$	35,877	$	31,357	$	80,661
	Net (loss) income per share, basic	$	(0.18	)	$	0.29	$	0.25	$	0.64
	Net (loss) income per share, diluted	$	(0.18	)	$	0.26	$	0.22	$	0.56
	2012
	Total revenue	$	272,770		$	280,607	$	285,874	$	309,265
	Gross profit	$	181,011		$	192,997	$	195,873	$	203,647
	Net income	$	26,202		$	23,401	$	29,748	$	71,903
	Net income per share, basic	$	0.21		$	0.19	$	0.24	$	0.58
	Net income per share, diluted	$	0.2		$	0.18	$	0.22	$	0.53

Unsolicited_Tender_Offer

Unsolicited Tender Offer	12 Months Ended
	Dec. 29, 2013
Unsolicited Tender Offer [Abstract]	'
Unsolicited Tender Offer [Text Block]	'
		Unsolicited Tender Offer
	On January 27, 2012, CKH Acquisition Corporation and Roche Holding Ltd. (together, “Roche”) commenced an unsolicited tender offer (Offer) to purchase all outstanding shares of the Company’s common stock for $44.50 per share. As more fully described in the Company’s Solicitation/Recommendation on Schedule 14D-9 filed with the SEC on February 7, 2012 in response to the Offer, the Company’s Board of Directors unanimously recommended that the Company’s stockholders reject the Offer and not tender their shares to Roche for purchase.
	On March 28, 2012, Roche revised the Offer to purchase all outstanding shares of the Company’s common stock for $51.00 per share. As more fully described in the Amendment No. 11 to Solicitation/Recommendation on Schedule 14D-9 filed with the SEC on April 2, 2012 in response to the revised Offer, the Company’s Board of Directors unanimously recommended that the Company’s stockholders reject the Roche offer and not tender their shares to Roche for purchase. The Offer expired, without being extended, on April 20, 2012.
	During the years ended December 29, 2013 and December 30, 2012, the Company recorded $13.6 million and $23.1 million, respectively in expenses in relation to the Offer, such expenses consisting primarily of legal, advisory, proxy solicitation, and other professional services fees.

SCHEDULE_II_VALUATION_AND_QUAL

SCHEDULE II - VALUATION AND QUALIFYING ACCOUNTS AND RESERVES	12 Months Ended
	Dec. 29, 2013
Valuation and Qualifying Accounts [Abstract]	'
Valuation and Qualifying Accounts and Reserves	'
	VALUATION AND QUALIFYING ACCOUNTS AND RESERVES
		Balance at		Additions Charged		Deductions(2)		Balance at
		Beginning of		to (Reductions from) Expense/				End of
		Period		Revenue(1)				Period
		(In thousands)
	Year ended December 29, 2013
	Allowance for doubtful accounts	$	4,280	(422	)	(178	)	$	3,680
	Year ended December 30, 2012
	Allowance for doubtful accounts	$	3,997	2,191		(1,908	)	$	4,280
	Year ended January 1, 2012
	Allowance for doubtful accounts	$	1,686	4,201		(1,890	)	$	3,997
	_______________________________________
	-1	Additions to and reductions from allowance for doubtful accounts are recorded to selling, general and administrative expense.
	-2	Deductions for allowance for doubtful accounts are for accounts receivable written off.

Organization_and_Summary_of_Si1

Organization and Summary of Significant Accounting Policies (Policies)	12 Months Ended
	Dec. 29, 2013
Organization and Summary of Significant Accounting Policies [Abstract]	'
Basis of Presentation	'
	Basis of Presentation
	The consolidated financial statements of the Company have been prepared in conformity with U.S. generally accepted accounting principles and include the accounts of the Company and its wholly-owned subsidiaries. All intercompany transactions and balances have been eliminated in consolidation.
Fiscal Year	'
	Fiscal Year
	The Company’s fiscal year is 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. Each of the years ended December 29, 2013, December 30, 2012, and January 1, 2012 were 52 weeks.
Use of Estimates	'
	Use of Estimates
	The preparation of financial statements requires that management make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue, expenses, and related disclosures of contingent assets and liabilities. Actual results could differ from those estimates.
Segment Information	'
	Segment Information
	For fiscal year 2013 and prior, the Company was organized in two operating segments for purposes of recording and reporting its financial results: Life Sciences and Diagnostics. The Life Sciences operating segment included all products and services related to the research market, namely the product lines based on the Company’s sequencing, BeadArray, and real-time polymerase chain reaction (PCR) technologies. The Diagnostics operating segment focused on the clinical and personalized application of the Company’s products and services for such uses as diagnosing disease, identifying genetic abnormalities, and identifying effective treatment therapies, with an initial emphasis on reproductive health and cancer. During all periods presented, the Diagnostics operating segment was immaterial to the financial statements as a whole. Accordingly, the financial results for both operating segments have been reported on an aggregate basis as one reportable segment.
	In late 2013, the Company announced organizational changes effective December 30, 2013 for the primary purpose of achieving scalability in business operations to support the growth in its strategic markets. The Company separated the roles of the Chief Executive Officer and the President, with core market and operational functions centralized and reporting to the President. Corporate functions and the President report to the CEO. As a result, the Company began operations as one operating segment as of December 30, 2013, and will continue to report under one reportable segment.
Fair Value Measurements	'
	Fair Value Measurements
	The Company determines the fair value of its assets and liabilities based on the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. Valuation techniques used to measure fair value maximize the use of observable inputs and minimize the use of unobservable inputs. The Company uses a fair value hierarchy with three levels of inputs, of which the first two are considered observable and the last unobservable, to measure fair value:
	•	Level 1 — Quoted prices in active markets for identical assets or liabilities.
	•	Level 2 — Inputs, other than Level 1, that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.
	•	Level 3 — Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.
	The carrying amounts of financial instruments such as cash and cash equivalents, accounts receivable, prepaid expenses and other current assets, accounts payable, and accrued liabilities, excluding acquisition related contingent consideration liabilities, approximate the related fair values due to the short-term maturities of these instruments.
Functional Currency	'
	Functional Currency
	The U.S. dollar is the functional currency of the Company’s international operations. The Company remeasures its foreign subsidiaries’ monetary assets and liabilities to the U.S. dollar and records the net gains or losses resulting from remeasurement in other expense, net in the consolidated statements of income.
Acquisitions	'
	Acquisitions
	The Company measures all assets acquired and liabilities assumed, including contingent considerations and all contractual contingencies, at fair value as of the acquisition date. Contingent purchase considerations to be settled in cash are remeasured to estimated fair value at each reporting period with the change in fair value recorded in acquisition related (gain) expense, net, a component of operating expenses. In addition, the Company capitalizes in-process research and development (IPR&D) and either amortizes it over the life of the product upon commercialization, or impairs it if the project is abandoned. Post-acquisition adjustments in deferred tax asset valuation allowances and liabilities for uncertain tax positions are recorded in current period income tax expense.
Cash Equivalents and Short-Term Investments	'
	Cash Equivalents and Short-Term Investments
	Cash equivalents are comprised of short-term, highly liquid investments with maturities of 90 days or less at the date of purchase.
	Short-term investments consist of U.S. Treasury securities, debt securities in U.S. government-sponsored entities, and corporate debt securities. Management classifies short-term investments as available-for-sale at the time of purchase and evaluates such classification as of each balance sheet date. All short-term investments are recorded at estimated fair value. Unrealized gains and losses for available-for-sale securities are included in accumulated other comprehensive income, a component of stockholders’ equity. The Company evaluates its investments to assess whether those with unrealized loss positions are other than temporarily impaired. Impairments are considered to be other than temporary if they are related to deterioration in credit risk or if it is likely that the Company will sell the securities before the recovery of their cost basis. Realized gains, losses, and declines in value judged to be other than temporary are determined based on the specific identification method and are reported in other income (expense), net in the consolidated statements of income.
Accounts Receivable	'
	Accounts Receivable
	Trade accounts receivable are recorded at the net invoice value and are not interest bearing. The Company considers receivables past due based on the contractual payment terms. The Company reserves specific receivables if collectibility is no longer reasonably assured. The Company also reserves a percentage of its trade receivable balance based on collection history and current economic trends that might impact the level of future credit losses. The Company re-evaluates such reserves on a regular basis and adjusts its reserves as needed. Once a receivable is deemed to be uncollectible, such balance is charged against the reserve.
Inventory	'
	Inventory
	Inventory is stated at the lower of cost or market, on a first in, first out basis. Inventory includes raw materials and finished goods that may be used in the research and development process and such items are expensed as consumed or expired. Provisions for slow moving, excess, and obsolete inventories are estimated based on product life cycles, quality issues, historical experience, and usage forecasts.
Property and Equipment	'
	Property and Equipment
	Property and equipment are stated at cost, subject to review of impairment, and depreciated over the estimated useful lives of the assets, which generally range from three to seven years, using the straight-line method. Amortization of leasehold improvements is recorded over the shorter of the lease term or the estimated useful life of the related assets. Maintenance and repairs are charged to operations as incurred. When assets are sold, or otherwise disposed of, the cost and related accumulated depreciation are removed from the accounts and any gain or loss is included in operating expense.
Leases	'
	Leases
	Leases are reviewed and classified as capital or operating at their inception. The Company records rent expense on a straight-line basis over the term of the lease, which includes the construction build-out period and lease extension periods, if appropriate. The difference between rent payments and straight-line rent expense is recorded as deferred rent in accrued liabilities and other long-term liabilities. Landlord allowances are amortized on a straight-line basis over the lease term as a reduction to rent expense. The Company capitalizes leasehold improvements and amortizes the value over the shorter of the lease term or expected useful lives.
	Headquarter relocation expenses consisted of expenses such as accelerated depreciation expense, impairment of assets, additional rent expense during the transition period when both the new and former headquarter facilities were occupied, moving expenses, cease-use losses, and accretion of interest expense on lease exit liability.
	In 2012, the Company completed the relocation of its headquarters to another facility in San Diego, California. The Company recorded accelerated depreciation expense for leasehold improvements at its former headquarter facility based on the reassessed useful lives of less than a year. The Company recorded cease-use losses and the corresponding facility exit obligation upon vacating its former headquarters, calculated as the present value of the remaining lease obligation offset by estimated sublease rental receipts during the remaining lease period, adjusted for deferred items and estimated lease incentives. The key assumptions used in the calculation include the amount and timing of estimated sublease rental receipts, and the risk-adjusted discount rate.
Goodwill, Intangible Assets and Other Long-Lived Assets	'
	Goodwill, Intangible Assets and Other Long-Lived Assets
	Goodwill, which has an indefinite useful life, represents the excess of cost over fair value of net assets acquired. The change in the carrying value of goodwill during the year ended December 29, 2013 was due to goodwill recorded in connection with acquisitions. Goodwill is reviewed for impairment at least annually during the second quarter, or more frequently if an event occurs indicating the potential for impairment. During its goodwill impairment review, the Company may assess qualitative factors to determine whether it is more likely than not that the fair value of its reporting unit is less than its carrying amount, including goodwill. The qualitative factors include, but are not limited to, macroeconomic conditions, industry and market considerations, and the overall financial performance of the Company. If, after assessing the totality of these qualitative factors, the Company determines that it is not more likely than not that the fair value of its reporting unit is less than its carrying amount, then no additional assessment is deemed necessary. Otherwise, the Company proceeds to perform the two-step test for goodwill impairment. The first step involves comparing the estimated fair value of the reporting unit with its carrying value, including goodwill. If the carrying amount of the reporting unit exceeds its fair value, the Company performs the second step of the goodwill impairment test to determine the amount of loss, which involves comparing the implied fair value of the goodwill to the carrying value of the goodwill. The Company may also elect to bypass the qualitative assessment in a period and elect to proceed to perform the first step of the goodwill impairment test. The Company performed its annual assessment for goodwill impairment in the second quarter of 2013, noting no impairment.
	IPR&D, which also has an indefinite useful life, is reviewed for impairment at least annually, or more frequently if an event occurs indicating the potential for impairment. The IPR&D impairment test requires the Company to assess the fair value of the asset as compared to its carrying value and record an impairment charge if the carrying value exceeds the fair value. During the second fiscal quarter of 2012, the Company recorded $21.4 million in impairment charges of IPR&D within research and development expenses in the consolidated statements of income, when resources previously assigned to the research project were re-directed with no plans for additional investments to be made to the project in the foreseeable future.
	The Company’s identifiable intangible assets are typically comprised of acquired core technologies, licensed technologies, customer relationships, and trade names. The cost of identifiable intangible assets with finite lives is generally amortized on a straight-line basis over the assets’ respective estimated useful lives.
	The Company regularly performs reviews to determine if any event has occurred that may indicate its intangible assets with finite useful lives and other long-lived assets are potentially impaired. If indicators of impairment exist, the Company performs an impairment test to assess the recoverability of the affected assets by determining whether the carrying amount of such assets exceeds the undiscounted expected future cash flows. If the affected assets are not recoverable, the Company estimates the fair value of the assets and records an impairment loss if the carrying value of the assets exceeds the fair value. Factors that may indicate potential impairment include a significant decline in the Company’s stock price and market capitalization compared to its net book value, significant changes in the ability of a particular asset to generate positive cash flows the Company’s strategic business objectives, and the pattern of utilization of a particular asset.
	During 2013, the Company decided to discontinue its Eco and NuPCR product lines to better align its product portfolio with its core strategy. As a result, the Company recorded a total impairment charge of $25.2 million in cost of product revenue, $22.9 million of which related to identifiable intangible assets, including developed technology and license agreements.
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 derivatives 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 December 29, 2013, the Company had foreign exchange forward contracts in place to hedge exposures in the euro, Japanese yen, and Australian dollar. As of December 29, 2013 and December 30, 2012, the total notional amount of outstanding forward contracts in place for foreign currency purchases was $54.7 million and $51.2 million, respectively. Non-designated foreign exchange forward contract related gain was $3.5 million for the year ended December 29, 2013 and immaterial for the years ended December 30, 2012 and January 1, 2012.
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 its 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 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 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.
	During the fiscal year ended January 1, 2012, the Company completed its Genome Analyzer trade-in program that enabled certain Genome Analyzer customers to trade in their Genome Analyzer and receive a discount on the purchase of a HiSeq 2000. The incentive was limited to customers who had purchased a Genome Analyzer prior to the beginning of the incentive program in early 2010 and was the only significant trade-in program offered by the Company.  The Company accounted for HiSeq 2000 discounts related to the Genome Analyzer trade-in program as reductions to revenue upon recognition of the HiSeq 2000 sales revenue, which is later than the date the trade-in program was launched.
	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.
Share-Based Compensation	'
	Share-Based Compensation
	The Company uses the Black-Scholes-Merton option-pricing model to estimate the fair value of stock options granted and stock purchases under the Employee Stock Purchase Plan (ESPP). This model incorporates various assumptions including expected volatility, expected term of an award, expected dividends, and the risk-free interest rates. The Company determines the expected volatility by equally weighing the historical and implied volatility of the Company’s common stock. The historical volatility of the Company’s common stock over the most recent period is generally commensurate with the estimated expected term of the Company’s stock awards, adjusted for the impact of unusual fluctuations not reasonably expected to recur and other relevant factors. The implied volatility is calculated from the implied market volatility of exchange-traded call options on the Company’s common stock. The expected term of an award is based on historical forfeiture experience, exercise activity, and on the terms and conditions of the stock awards. The expected dividend yield is determined to be 0% given that the Company has never declared or paid cash dividends on its common stock and does not anticipate paying such cash dividends. The risk-free interest rate is based upon U.S. Treasury securities with remaining terms similar to the expected term of the share-based awards. The fair value of restricted stock units granted is based on the closing market price of the Company’s common stock on the date of grant. The Company recognizes the fair value of share-based compensation on a straight-line basis over the requisite service periods of the awards.
Shipping and Handling Expenses	'
	Shipping and Handling Expenses
	Shipping and handling expenses are included in cost of product revenue.
Research and Development	'
	Research and Development
	Research and development expenses include personnel expenses, contractor fees, license fees, facilities costs, and utilities. Expenditures relating to research and development are expensed in the period incurred.
Advertising Costs	'
	Advertising Costs
	The Company expenses advertising costs as incurred. Advertising costs were $14.5 million, $10.5 million, and $9.4 million for the years ended December 29, 2013, December 30, 2012, and January 1, 2012, respectively.
Restructuring Charges	'
	Restructuring Charges
	During the year ended January 1, 2012, the Company announced and executed a restructuring plan to reduce the Company’s workforce and to consolidate certain facilities. The Company measured and accrued the liabilities associated with employee separation costs at fair value as of the date the plan was announced and terminations were communicated to employees, which primarily consisted of severance pay and other separation costs such as outplacement services and benefits.
	The fair value measurement of restructuring related liabilities requires certain assumptions and estimates to be made by the Company, such as the retention period of certain employees, the timing and amount of sublease income on properties to be vacated, and the operating costs to be paid until lease termination. It is the Company’s policy to use the best estimates based on facts and circumstances available at the time of measurement, review the assumptions and estimates periodically, and adjust the liabilities when necessary.
Income Taxes	'
	Income Taxes
	The provision for income taxes is computed using the asset and liability method, under which deferred tax assets and liabilities are recognized for the expected future tax consequences of temporary differences between the financial reporting and tax bases of assets and liabilities, and for the expected future tax benefit to be derived from tax loss and credit carryforwards. Deferred tax assets and liabilities are determined using the enacted tax rates in effect for the years in which those tax assets are expected to be realized. The effect of a change in tax rates on deferred tax assets and liabilities is recognized in the provision for income taxes in the period that includes the enactment date.
	Deferred tax assets are regularly assessed to determine the likelihood they will be recovered from future taxable income. A valuation allowance is established when the Company believes it is more likely than not the future realization of all or some of a deferred tax asset will not be achieved. In evaluating the ability to recover deferred tax assets within the jurisdiction which they arise the Company considers all available positive and negative evidence. Factors reviewed include the cumulative pre-tax book income for the past three years, scheduled reversals of deferred tax liabilities, history of earnings and reliable forecasting, projections of pre-tax book income over the foreseeable future, and the impact of any feasible and prudent tax planning strategies.
	The Company recognizes excess tax benefits associated with share-based compensation to stockholders’ equity only when realized. When assessing whether excess tax benefits relating to share-based compensation have been realized, the Company follows the with-and-without approach excluding any indirect effects of the excess tax deductions. Under this approach, excess tax benefits related to share-based compensation are not deemed to be realized until after the utilization of all other tax benefits available to the Company.
	The Company recognizes the impact of a tax position in the financial statements only if that position is more likely than not of being sustained upon examination by taxing authorities, based on the technical merits of the position. Any interest and penalties related to uncertain tax positions will be reflected in income tax expense.
Net Income per Share	'
	Net Income per Share
	Basic net income per share is computed based on the weighted average number of common shares outstanding during the period. Diluted net income 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 therefore excluded.
	The following table presents the calculation of weighted average number of shares used to calculate basic and diluted net income per share (in thousands):
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	Weighted average shares outstanding	125,076			122,999			123,399
	Effect of dilutive potential common shares from:
	Convertible senior notes	1,340			967			3,783
	Equity awards	4,404			3,906			4,703
	Warrants	9,116			5,821			7,052
	Weighted average shares used in calculating diluted net income per share	139,936			133,693			138,937
	Potentially dilutive shares excluded from calculation due to anti-dilutive effect	996			2,556			2,418
Accumulated Other comprehensive income	'
	Accumulated Other Comprehensive Income
	Comprehensive income is comprised of net income and other comprehensive income. Accumulated other comprehensive income on the consolidated balance sheets at December 29, 2013 and December 30, 2012 includes accumulated foreign currency translation adjustments and unrealized gains and losses on the Company’s available-for-sale securities.
	The components of accumulated other comprehensive income are as follows (in thousands):
		December 29,				December 30,
		2013				2012
	Foreign currency translation adjustments	$	1,289			$	1,289
	Unrealized (loss) gain on available-for-sale securities, net of deferred tax	(55		)		834
	Total accumulated other comprehensive income	$	1,234			$	2,123

Organization_and_Summary_of_Si2

Organization and Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 29, 2013
Organization and Summary of Significant Accounting Policies [Abstract]	'
Weighted-average shares used to calculate basic and diluted net income per share	'
	The following table presents the calculation of weighted average number of shares used to calculate basic and diluted net income per share (in thousands):
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	Weighted average shares outstanding	125,076			122,999			123,399
	Effect of dilutive potential common shares from:
	Convertible senior notes	1,340			967			3,783
	Equity awards	4,404			3,906			4,703
	Warrants	9,116			5,821			7,052
	Weighted average shares used in calculating diluted net income per share	139,936			133,693			138,937
	Potentially dilutive shares excluded from calculation due to anti-dilutive effect	996			2,556			2,418
Accumulated other comprehensive income	'
	The components of accumulated other comprehensive income are as follows (in thousands):
		December 29,				December 30,
		2013				2012
	Foreign currency translation adjustments	$	1,289			$	1,289
	Unrealized (loss) gain on available-for-sale securities, net of deferred tax	(55		)		834
	Total accumulated other comprehensive income	$	1,234			$	2,123

Balance_Sheet_Account_Details_

Balance Sheet Account Details (Tables)	12 Months Ended
	Dec. 29, 2013
Balance Sheet Account Details [Abstract]	'
Short-term Investments	'
	The following is a summary of short-term investments (in thousands):
		December 29, 2013												December 30, 2012
					Gross			Gross								Gross		Gross
		Amortized			Unrealized			Unrealized			Estimated			Amortized		Unrealized		Unrealized			Estimated
		Cost			Gains			Losses			Fair Value			Cost		Gains		Losses			Fair Value
	Available-for-sale securities:
	Debt securities in government-sponsored entities	$	82,226		$	18		$	(101	)	$	82,143		$	314,638	$	251	$	(16	)	$	314,873
	Corporate debt securities	342,034			312			(376		)	341,970			471,989		1,059		(187		)	472,861
	U.S. Treasury securities	29,795			58			—			29,853			128,256		233		—			128,489
	Total available-for-sale securities	$	454,055		$	388		$	(477	)	$	453,966		$	914,883	$	1,543	$	(203	)	$	916,223
Available-for-sale securities in unrealized loss positions	'
	The following table shows the estimated fair values and the gross unrealized losses of the Company’s available-for-sale securities that were in an unrealized loss position for less than twelve months as of December 29, 2013 and December 30, 2012, respectively, aggregated by investment category (in thousands):
		December 29, 2013						December 30, 2012
		Estimated Fair Value			Gross			Estimated Fair Value			Gross
					Unrealized						Unrealized
					Losses						Losses
	Debt securities in government-sponsored entities	$	73,362		$	(101	)	$	28,176		$	(16	)
	Corporate debt securities	168,118			(373		)	130,224			(187		)
	Total	$	241,480		$	(474	)	$	158,400		$	(203	)
Contractual maturities of available-for-sale securities	'
	Contractual maturities of available-for-sale debt securities as of December 29, 2013 are as follows (in thousands):
		Estimated Fair Value
	Due within one year	$	127,081
	After one but within five years	326,885
	Total	$	453,966
Accounts receivable	'
	Accounts receivable consist of the following (in thousands):
		December 29,			December 30,
		2013			2012
	Accounts receivable from product and service sales	$	241,360		$	217,369
	Other receivables	1,266			1,886
	Total accounts receivable, gross	242,626			219,255
	Allowance for doubtful accounts	(3,680		)	(4,280		)
	Total accounts receivable, net	$	238,946		$	214,975
Inventory	'
	Inventory consists of the following (in thousands):
		December 29,			December 30,
		2013			2012
	Raw materials	$	57,398		$	61,665
	Work in process	70,016			75,675
	Finished goods	26,685			21,378
	Total inventory	$	154,099		$	158,718
Property and equipment	'
	Property and equipment, net consists of the following (in thousands):
		December 29,			December 30,
		2013			2012
	Leasehold improvements	$	104,571		$	87,734
	Machinery and equipment	175,340			158,112
	Computer hardware and software	73,544			58,313
	Furniture and fixtures	10,511			8,022
	Building	7,670			—
	Construction in progress	8,531			7,390
	Total property and equipment, gross	380,167			319,571
	Accumulated depreciation	(177,501		)	(153,404		)
	Total property and equipment, net	$	202,666		$	166,167
Restructuring Activities	'
	A summary of the pre-tax charges and total costs associated with the initiative is as follows (in thousands):
		Employee Separation costs			Facilities Exit Costs			Other Costs			Total
	Amount recorded in accrued liabilities as of January 1, 2012	$	3,496		$	—		$	30		$	3,526
	Additional expenses	2,780			221			521			3,522
	Cash payments	(6,276		)	(221		)	(551		)	(7,048		)
	Amount recorded in accrued liabilities as of December 30, 2012	$	—		$	—		$	—		$	—
	Cumulative expense recorded since inception in restructuring expense	$	10,463		$	221		$	974		$	11,658
Accrued liabilities	'
	Accrued liabilities consist of the following (in thousands):
		December 29,			December 30,
		2013			2012
	Accrued compensation expenses	$	82,705		$	59,864
	Deferred revenue, current portion	50,834			55,817
	Accrued taxes payable	30,435			23,021
	Customer deposits	13,569			13,765
	Reserve for product warranties	10,407			10,136
	Acquisition related contingent consideration liability, current portion	6,719			9,490
	Facility exit obligation, current portion	5,570			8,063
	Unsettled short-term investment purchase	—			9,154
	Other	18,881			12,567
	Total accrued liabilities	$	219,120		$	201,877

Acquisitions_Tables

Acquisitions (Tables)	12 Months Ended
	Dec. 29, 2013
Business Combinations [Abstract]	'
Allocation of the purchase price to the assets acquired and liabilities assumed	'
	As of December 29, 2013, the allocation of the purchase price to the assets acquired and liabilities assumed on the acquisition date was as follows (in thousands):
		Allocation of purchase price
	Cash and cash equivalents	$	9,151
	Accounts receivable	2,801
	Inventory	1,110
	Prepaid expenses and other current assets	979
	Property and equipment	12,083
	Other assets	978
	Intangible assets	176,490
	Goodwill	227,453
	Accounts payable	(2,539		)
	Accrued liabilities	(3,803		)
	Lease financing obligation	(9,695		)
	Deferred tax liability	(18,741		)
	Total purchase price	$	396,267
Fair value of identifiable intangible assets acquired	'
	The following table summarizes the fair value of identifiable intangible assets acquired (amounts in thousands):
		Weighted Average Useful Lives (in years)		Fair Value
	Developed technology	13		$	170,200
	Customer relationships	5		4,690
	Trade name	2		1,600
	Total intangible assets acquired, excluding goodwill			$	176,490
Pro forma information	'
	The following unaudited pro forma information presents the consolidated results of operations of the Company as if the acquisitions completed during the year ended December 29, 2013 had occurred at the beginning of the applicable annual reporting period, with pro forma adjustments to give effect to intercompany transactions to be eliminated, amortization of intangible assets, share-based compensation, and transaction costs directly associated with the acquisitions (in thousands, except per share amounts):
		Years Ended
		December 29,				December 30,
		2013				2012
	Net revenues	$	1,433,935			$	1,161,241
	Net income	$	113,869			$	92,645
	Net income per share-basic	$	0.91			$	0.75
	Net income per share-diluted	$	0.81			$	0.69
Contingent compensation expense and IPR&D charges	'
	Contingent compensation expenses and IPR&D charges as a result of acquisitions consist of the following (in thousands):
		Years Ended
		December 29,				December 30,		January 1,
		2013				2012		2012
	Contingent compensation expense, included in research and development expense	$	544			$	3,419	$	4,799
	Contingent compensation expense, included in selling, general and administrative expense	13,066				5,732		1,258
	Total contingent compensation expense	$	13,610			$	9,151	$	6,057
	IPR&D, included in acquisition related expense (gain), net	$	—			$	—	$	5,425

Intangible_Assets_Tables

Intangible Assets (Tables)	12 Months Ended
	Dec. 29, 2013
Intangible Assets, Net (Excluding Goodwill) [Abstract]	'
Identifiable Intangible Assets	'
	The following is a summary of the Company’s identifiable intangible assets as of the respective balance sheet dates (in thousands):
		December 29, 2013									December 30, 2012
		Gross				Accumulated			Intangibles,		Gross		Accumulated			Intangibles,
		Carrying				Amortization			Net		Carrying		Amortization			Net
		Amount									Amount
	Licensed technologies	$	48,361			$	(31,927	)	$	16,434	$	47,329	$	(25,471	)	$	21,858
	Core technologies	321,700				(45,534		)	276,166		99,800		(27,427		)	72,373
	Customer relationships	26,770				(7,376		)	19,394		18,780		(2,214		)	16,566
	License agreements	18,917				(4,947		)	13,970		14,404		(3,933		)	10,471
	Trade name	11,800				(6,591		)	5,209		9,600		(672		)	8,928
	Total intangible assets, net	$	427,548			$	(96,375	)	$	331,173	$	189,913	$	(59,717	)	$	130,196
Acquired Identifiable Intangible Assets	'
	Additions to intangible assets during the year ended December 29, 2013 were primarily due to acquisitions during the year. The components of such intangibles assets acquired are as follows (in thousands):
		Weighted Average		Gross
		Useful Lives		Carrying
		(years)		Amount
	Core technologies	12		$	249,900
	License agreements	10		10,013
	Customer relationships	4		7,990
	Trade name	2		2,200
	Licensed technologies	5		1,032
	Total intangible asset additions			$	271,135
Estimated annual amortization of intangible assets	'
	The estimated annual amortization of intangible assets for the next five years is shown in the following table (in thousands). Actual amortization expense to be reported in future periods could differ from these estimates as a result of acquisitions, divestitures, asset impairments, among other factors.
		Estimated Annual Amortization
	2014	$	49,376
	2015	45,974
	2016	40,582
	2017	36,106
	2018	27,310
	Thereafter	131,825
	Total	$	331,173

Fair_Value_Measurement_Tables

Fair Value Measurement (Tables)	12 Months Ended
	Dec. 29, 2013
Fair Value Disclosures [Abstract]	'
Fair value measurements	'
	The following table presents the Company’s fair value hierarchy for assets and liabilities measured at fair value on a recurring basis as of December 29, 2013 and December 30, 2012, respectively (in thousands):
		December 29, 2013									December 30, 2012
		Level 1			Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
	Assets:
	Money market funds (cash equivalent)	$	478,755		$	—	$	—	$	478,755	$	252,126	$	—	$	—	$	252,126
	Debt securities in government-sponsored entities	—			82,143		—		82,143		—		314,873		—		314,873
	Corporate debt securities	—			341,970		—		341,970		—		472,861		—		472,861
	U.S. Treasury securities	29,853			—		—		29,853		128,489		—		—		128,489
	Deferred compensation plan assets	—			17,805		—		17,805		—		13,626		—		13,626
	Total assets measured at fair value	$	508,608		$	441,918	$	—	$	950,526	$	380,615	$	801,360	$	—	$	1,181,975
	Liabilities:
	Acquisition related contingent consideration liabilities	$	—		$	—	$	49,480	$	49,480	$	—	$	—	$	12,519	$	12,519
	Deferred compensation liability	—			14,957		—		14,957		—		12,071		—		12,071
	Total liabilities measured at fair value	$	—		$	14,957	$	49,480	$	64,437	$	—	$	12,071	$	12,519	$	24,590
Changes in estimated fair value of contingent consideration liabilities	'
	Changes in estimated fair value of contingent consideration liabilities from January 2, 2011 through December 29, 2013 are as follows (in thousands):
		Contingent
		Consideration
		Liability
		(Level 3 Measurement)
	Balance as of January 2, 2011	$	3,738
	Acquisition of Epicentre	7,400
	Change in estimated fair value, recorded in acquisition related (gain) expense, net	(4,500		)
	Balance as of January 1, 2012	6,638
	Acquisition of BlueGnome	7,500
	Change in estimated fair value, recorded in acquisition related (gain) expense, net	1,975
	Cash payments	(3,594		)
	Balance as of December 30, 2012	12,519
	Additional liability recorded for current period acquisitions	60,184
	Change in estimated fair value, recorded in acquisition related (gain) expense, net	(18,784		)
	Cash payments	(4,439		)
	Balance as of December 29, 2013	$	49,480

Convertible_Senior_Notes_Table

Convertible Senior Notes (Tables)	12 Months Ended
	Dec. 29, 2013
Debt Disclosure [Abstract]	'
Schedule of Extinguishment of Debt	'
	The following table summarizes information about the conversion of the 2014 Notes during year ended December 29, 2013 (in thousands, except percentages):
			2014 Notes
	Cash paid for principal of notes converted		$	10,555
	Conversion value over principal amount paid in shares of common stock		$	21,217
	Number of shares of common stock issued upon conversion		317
	Loss on extinguishment of debt		$	555
	Effective interest rate used to measure fair value of converted notes upon conversion		0.5% - 0.8%
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 and 2016 Notes (dollars in thousands). The fair values of the respective notes outstanding were measured based on quoted market prices.
		December 29, 2013			December 30, 2012
	Principal amount of convertible notes outstanding	$	949,570		$	960,125
	Unamortized discount of liability component	(80,977		)	(117,752		)
	Net carrying amount of liability component	868,593			842,373
	Less: current portion	(29,288		)	(36,967		)
	Long-term debt	$	839,305		$	805,406
	Conversion option subject to cash settlement	$	282		$	3,158
	Carrying value of equity component, net of issuance costs	$	274,304		$	271,966
	Fair value of outstanding notes	$	1,428,743		$	993,916
	Weighted average remaining amortization period of discount on the liability component	2 years			3 years

Commitments_Tables

Commitments (Tables)	12 Months Ended
	Dec. 29, 2013
Commitments and Contingencies Disclosure [Abstract]	'
Future minimom payments under operating leases	'
	Annual future minimum payments under operating leases as of December 29, 2013 were as follows (in thousands):
		Operating Leases			Sublease Income			Net Operating Leases
	2014	$	29,526		$	(2,478	)	$	27,048
	2015	29,463			(2,552		)	26,911
	2016	29,327			(2,629		)	26,698
	2017	29,383			(2,708		)	26,675
	2018	29,601			(2,789		)	26,812
	Thereafter	395,342			(14,708		)	380,634
	Total minimum lease payments	$	542,642		$	(27,864	)	$	514,778
Facility exit obligations	'
	Changes in the facility exit obligation from January 1, 2012 through December 29, 2013 are as follows (in thousands):
		Headquarter Facility Exit Obligation
	Balance as of January 1, 2012:	$	25,049
	Adjustment to facility exit obligation	24,878
	Accretion of interest expense	2,129
	Cash payments	(6,704		)
	Balance as of December 30, 2012:	45,352
	Adjustment to facility exit obligation	(114		)
	Accretion of interest expense	2,738
	Cash payments	(9,758		)
	Balance as of December 29, 2013	$	38,218
Reserve for product warranties	'
	Changes in the Company’s reserve for product warranties from January 2, 2011 through December 29, 2013 are as follows (in thousands):
		Warranty Reserve
	Balance as of January 2, 2011	$	16,761
	Additions charged to cost of revenue	17,913
	Repairs and replacements	(22,708		)
	Balance as of January 1, 2012	11,966
	Additions charged to cost of revenue	17,279
	Repairs and replacements	(19,109		)
	Balance as of December 30, 2012	10,136
	Additions charged to cost of revenue	15,674
	Repairs and replacements	(15,403		)
	Balance as of December 29, 2013	$	10,407

Sharebased_Compensation_Expens1

Share-based Compensation Expense (Tables)	12 Months Ended
	Dec. 29, 2013
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Share-based compensation expense for all stock awards	'
	Total share-based compensation expense for all stock awards consists of the following (in thousands):
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	Cost of product revenue	$	6,223		$	7,575		$	6,951
	Cost of service and other revenue	777			461			695
	Research and development	37,439			30,879			32,105
	Selling, general and administrative	61,387			55,409			52,341
	Share-based compensation expense before taxes	105,826			94,324			92,092
	Related income tax benefits	(32,819		)	(30,759		)	(32,168		)
	Share-based compensation expense, net of taxes	$	73,007		$	63,565		$	59,924
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'
	The assumptions used for the specified reporting periods and the resulting estimates of weighted-average fair value per share of options granted and for stock purchased under the ESPP during those periods are as follows:
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	Stock options granted:
	Risk-free interest rate	0.14 - 1.86%			0.56 - 0.93%			0.85 - 2.23%
	Expected volatility	30 - 44%			41 - 48%			41 - 53%
	Expected term	0.8 - 9.4 years			4.0 - 6.6 years			4.7 - 5.5 years
	Expected dividends	—			—			—
	Weighted average fair value per share	$	40.66		$	15.47		$	27.47
	Stock purchased under the ESPP:
	Risk-free interest rate	0.08 - 0.15%			0.09 - 0.17%			0.16 - 0.30%
	Expected volatility	31 - 32%			33 - 64%			43 - 48%
	Expected term	0.5 - 1.0 year			0.5 - 1.0 year			0.5 - 1.0 year
	Expected dividends	—			—			—
	Weighted average fair value per share	$	19.3		$	16.45		$	20.08

Stockholders_Equity_Tables

Stockholders' Equity (Tables)	12 Months Ended
	Dec. 29, 2013
Equity [Abstract]	'
Stock option activity under all stock option plans	'
	The Company’s stock option activity under all stock option plans from January 2, 2011 through December 29, 2013 is as follows:
		Options		Weighted-
		(in thousands)		Average
				Exercise Price
	Outstanding at January 2, 2011	11,882		$	22.83
	Granted	1,399		64.98
	Exercised	(2,784	)	17.98
	Cancelled	(119	)	33.49
	Outstanding at January 1, 2012	10,378		29.69
	Granted	251		40.79
	Exercised	(2,071	)	20.34
	Cancelled	(207	)	39.18
	Outstanding at December 30, 2012	8,351		32.1
	Granted	512		14.74
	Exercised	(3,006	)	27.7
	Cancelled	(133	)	41.8
	Outstanding at December 29, 2013	5,724		$	32.64
Restricted stock activity	'
	A summary of the Company’s restricted stock activity and related information from January 2, 2011 through December 29, 2013 is as follows (in thousands, except per share amounts):
										Weighted Average
										Grant-Date Fair Value per Share
		RSA		RSU			PSU			RSA		RSU		PSU
	Outstanding at January 2, 2011	—		3,109			—			$	—	$	40.39	$	—
	Awarded	230		1,550			—			65.95		42.02		—
	Vested	—		(827	)		—			—		36.47		—
	Cancelled	—		(356	)		—			—		42.15		—
	Outstanding at January 1, 2012	230		3,476			—			65.95		41.87		—
	Awarded	312		1,640			599			47.91		48.52		49.66
	Vested	(77	)	(1,062	)		—			65.95		38.48		—
	Cancelled	—		(394	)		(12	)		—		45.05		50.54
	Outstanding at December 30, 2012	465		3,660			587			53.84		45.49		49.64
	Awarded	—		1,532			584			—		77.53		59.16
	Vested	(217	)	(1,308	)		—			54.27		42.97		—
	Cancelled	—		(256	)		(70	)		—		49.24		50.42
	Outstanding at December 29, 2013	248		3,628			1,101			$	53.46	$	59.66	$	54.64
Pre-tax intrinsic values of all outstanding restricted and performance stock and total fair values of vested restricted and performance stock	'
	Pre-tax intrinsic values of all outstanding restricted and performance stock and total fair values of vested restricted and performance stock are as follows (in thousands):
		Years Ended
		December 29,			December 30,				January 1,
		2013			2012				2012
	Pre-tax intrinsic value of outstanding restricted and performance stock:
	RSA	$	27,384		$	25,437			$	6,986
	RSU	400,421			200,383				105,944
	PSU	121,555			32,149				—
	Fair value of restricted and performance stock vested:
	RSA	$	11,750		$	5,039			—
	RSU	56,212			40,870				30,155
	PSU	—			—				—

Income_Taxes_Tables

Income Taxes (Tables)	12 Months Ended
	Dec. 29, 2013
Income Tax Disclosure [Abstract]	'
Income before income taxes summarized by region	'
	The income (loss) before income taxes summarized by region is as follows (in thousands):
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	United States	$	(53,703	)	$	102,296		$	(7,100	)
	Foreign	213,017			120,312			140,145
	Total income before income taxes	$	159,314		$	222,608		$	133,045
Provision for income taxes	'
	The provision for income taxes consists of the following (in thousands):
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	Current:
	Federal	$	78,419		$	57,285		$	43,161
	State	8,854			10,121			3,958
	Foreign	39,416			31,504			24,154
	Total current provision	126,689			98,910			71,273
	Deferred:
	Federal	(69,102		)	(7,724		)	(22,738		)
	State	(15,222		)	(7,708		)	(8,050		)
	Foreign	(8,359		)	(12,124		)	5,932
	Total deferred benefit	(92,683		)	(27,556		)	(24,856		)
	Total tax provision	$	34,006		$	71,354		$	46,417
Provision for income taxes reconciles to the amount computed by applying the federal statutory rate to income before taxes	'
	The provision for income taxes reconciles to the amount computed by applying the federal statutory rate to income before taxes as follows (in thousands):
		Years Ended
		December 29,			December 30,			January 1,
		2013			2012			2012
	Tax at federal statutory rate	$	55,760		$	77,913		$	46,566
	State, net of federal benefit	647			4,056			(49		)
	Research and other credits	(10,977		)	(2,613		)	(7,418		)
	Acquired in-process research & development	—			137			1,989
	Change in valuation allowance	10,544			(37		)	(688		)
	Permanent differences	1,120			2,380			1,668
	Change in fair value of contingent consideration	(3,859		)	—			(1,311		)
	Impact of foreign operations	(18,006		)	(11,470		)	5,579
	Other	(1,223		)	988			81
	Total tax provision	$	34,006		$	71,354		$	46,417
Significant components of deferred tax assets and liabilities	'
	Significant components of the Company’s deferred tax assets and liabilities are as follows (in thousands):
		December 29,			December 30,
		2013			2012
	Deferred tax assets:
	Net operating losses	$	66,969		$	2,564
	Tax credits	36,277			16,447
	Other accruals and reserves	103,539			47,306
	Stock compensation	36,728			39,175
	Inventory adjustments	9,034			8,977
	Impairment of cost-method investment	3,540			1,406
	Other amortization	9,571			5,195
	Other	14,704			13,469
	Total gross deferred tax assets	280,362			134,539
	Valuation allowance on deferred tax assets	(19,132		)	(1,756		)
	Total deferred tax assets	261,230			132,783
	Deferred tax liabilities:
	Purchased intangible amortization	(98,671		)	(20,116		)
	Convertible debt	(27,821		)	(38,910		)
	Property and equipment	(13,311		)	(10,867		)
	Other	(6,349		)	(6,682		)
	Total deferred tax liabilities	(146,152		)	(76,575		)
	Net deferred tax assets	$	115,078		$	56,208
Summary of the gross amount of uncertain tax positions	'
	The following table summarizes the gross amount of the Company’s uncertain tax positions (in thousands):
		December 29,			December 30,			January 1,
		2013			2012			2012
	Balance at beginning of year	$	37,585		$	28,396		$	22,729
	Increases related to prior year tax positions	4,794			2,573			875
	Decreases related to prior year tax positions	(223		)	(69		)	(382		)
	Increases related to current year tax positions	7,503			6,685			5,174
	Decreases related to lapse of statute of limitations	(613		)	—			—
	Balance at end of year	$	49,046		$	37,585		$	28,396

Segment_Information_Geographic1

Segment Information, Geographic Data, and Significant Customers (Tables)	12 Months Ended
	Dec. 29, 2013
Segment Reporting [Abstract]	'
Revenue by region	'
	The Company had revenue in the following regions for the years ended December 29, 2013, December 30, 2012, and January 1, 2012 (in thousands):
		Years Ended
		December 29,		December 30,		January 1,
		2013		2012		2012
	United States	$	714,662	$	568,443	$	528,723
	Europe	354,682		291,404		277,971
	Asia-Pacific	276,442		232,498		197,005
	Other markets	75,392		56,171		51,836
	Total	$	1,421,178	$	1,148,516	$	1,055,535
Net long-lived assets consisting of property and equipment by region	'
	The Company had net long-lived assets consisting of property and equipment in the following regions as of December 29, 2013 and December 30, 2012 (in thousands):
		December 29,		December 30,
		2013		2012
	United States	$	150,470	$	126,749
	United Kingdom	24,122		21,740
	Singapore	21,311		12,504
	Other countries	6,763		5,174
	Total	$	202,666	$	166,167

Quarterly_Financial_Informatio1

Quarterly Financial Information (unaudited) (Tables)	12 Months Ended
	Dec. 29, 2013
Quarterly Financial Information Disclosure [Abstract]	'
Schedule of Quarterly Financial Information [Table Text Block]	'
	Summarized quarterly data for fiscal years 2013 and 2012 are as follows (in thousands except per share data):
		First Quarter			Second Quarter		Third Quarter		Fourth Quarter
	2013
	Total revenue	$	330,958		$	346,094	$	356,800	$	387,326
	Gross profit	$	219,292		$	223,409	$	209,940	$	259,246
	Net (loss) income	$	(22,587	)	$	35,877	$	31,357	$	80,661
	Net (loss) income per share, basic	$	(0.18	)	$	0.29	$	0.25	$	0.64
	Net (loss) income per share, diluted	$	(0.18	)	$	0.26	$	0.22	$	0.56
	2012
	Total revenue	$	272,770		$	280,607	$	285,874	$	309,265
	Gross profit	$	181,011		$	192,997	$	195,873	$	203,647
	Net income	$	26,202		$	23,401	$	29,748	$	71,903
	Net income per share, basic	$	0.21		$	0.19	$	0.24	$	0.58
	Net income per share, diluted	$	0.2		$	0.18	$	0.22	$	0.53

Organization_and_Summary_of_Si3

Organization and Summary of Significant Accounting Policies (Details)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Weighted average shares used to calculate basic and diluted net income per share [Line Items]	'	'	'
Weighted average shares outstanding	125,076	122,999	123,399
Convertible senior notes	1,340	967	3,783
Equity awards	4,404	3,906	4,703
Warrants	9,116	5,821	7,052
Weighted average shares used in calculating diluted net income per share	139,936	133,693	138,937
Potentially dilutive shares excluded from calculation due to anti-dilutive effect	996	2,556	2,418

Organization_and_Summary_of_Si4

Organization and Summary of Significant Accounting Policies (Details 1) (USD $)	Dec. 29, 2013	Dec. 30, 2012
In Thousands, unless otherwise specified
Accounting Policies [Abstract]	'	'
Foreign currency translation adjustments	$1,289	$1,289
Unrealized (loss) gain on available-for-sale securities, net of deferred tax	-55	834
Total accumulated other comprehensive income	$1,234	$2,123

Organization_and_Summary_of_Si5

Organization and Summary of Significant Accounting Policies (Details Textual) (USD $)	0 Months Ended	3 Months Ended	12 Months Ended
	Dec. 31, 2013	Jul. 01, 2012	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
	segments		segments
Operating Cycle	'	'	'P52W	'P52W	'P52W
Number of reportable segments	'	'	1	'	'
Number of operating segments	1	'	2	'	'
Number of future reportable segments	1	'	'	'	'
Maximum investment portfolio credit exposure per issuer at time of purchase	'	'	5.00%	'	'
Maximum investment portfolio credit exposure per industry sector at time of purchase	'	'	25.00%	'	'
Cash Equivalents and Short-term Investments, Maturity Period, Maximum1	'	'	'90 days	'	'
Impairment of IPR&D	'	$21,400,000	'	'	'
Impairments	'	'	25,214,000	21,438,000	'
Notional amount of outstanding forward contracts	'	'	54,700,000	51,200,000	'
Non-designated forward contract related loss	'	'	3,500,000	'	'
Instrument warranty period	'	'	'1 year	'	'
Expected dividend yield	'	'	0.00%	'	'
Advertising expense	'	'	14,500,000	10,500,000	9,400,000
Minimum [Member]	'	'	'	'	'
Useful life	'	'	'3 years	'	'
Consumable warranty period	'	'	'6 months	'	'
Product or service delivery period	'	'	'3 months	'	'
Maximum [Member]	'	'	'	'	'
Useful life	'	'	'7 years	'	'
Consumable warranty period	'	'	'12 months	'	'
Product or service delivery period	'	'	'6 months	'	'
Cost of Sales [Member]	'	'	'	'	'
Impairments	'	'	25,200,000	'	'
Intangible asset impairments	'	'	$22,900,000	'	'

Organization_and_Summary_of_Si6

Organization and Summary of Significant Accounting Policies (Details Texual 2)	12 Months Ended
	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Countries outside the United States | Sales Revenue, Segment [Member]	'	'	'
Concentration Risk [Line Items]	'	'	'
Concentration Risk, Percentage	50.00%	51.00%	50.00%
Countries outside the United States | Accounts Receivable [Member]	'	'	'
Concentration Risk [Line Items]	'	'	'
Concentration Risk, Percentage	52.00%	54.00%	'
European countries other than UK [Member] | Sales Revenue, Segment [Member]	'	'	'
Concentration Risk [Line Items]	'	'	'
Concentration Risk, Percentage	18.00%	'	'
Certain Southern European countries [Member] | Accounts Receivable [Member] | Maximum [Member]	'	'	'
Concentration Risk [Line Items]	'	'	'
Concentration Risk, Percentage	5.00%	'	'

Balance_Sheet_Account_Details_1

Balance Sheet Account Details (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	$454,055	$914,883
Available for sale securities, Gross Unrealized Gains	388	1,543
Available for sale securities, Gross Unrealized Losses	-477	-203
Total Estimated Fair Value	453,966	916,223
Debt securities in government sponsored entities [Member]	'	'
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	82,226	314,638
Available for sale securities, Gross Unrealized Gains	18	251
Available for sale securities, Gross Unrealized Losses	-101	-16
Total Estimated Fair Value	82,143	314,873
Corporate debt securities [Member]	'	'
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	342,034	471,989
Available for sale securities, Gross Unrealized Gains	312	1,059
Available for sale securities, Gross Unrealized Losses	-376	-187
Total Estimated Fair Value	341,970	472,861
U.S. Treasury securities [Member]	'	'
Available-for-sale securities:	'	'
Available for sale securities, Amortized Cost	29,795	128,256
Available for sale securities, Gross Unrealized Gains	58	233
Total Estimated Fair Value	$29,853	$128,489

Balance_Sheet_Account_Details_2

Balance Sheet Account Details (Details 1) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	$241,480	$158,400
Gross Unrealized Losses	-474	-203
Debt securities in government sponsored entities [Member]	'	'
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	73,362	28,176
Gross Unrealized Losses	-101	-16
Corporate debt securities [Member]	'	'
Available-for-sale securities gross unrealized loss position	'	'
Estimated Fair Value	168,118	130,224
Gross Unrealized Losses	($373)	($187)

Balance_Sheet_Account_Details_3

Balance Sheet Account Details (Details 2) (USD $)	Dec. 29, 2013	Dec. 30, 2012
In Thousands, unless otherwise specified
Available-for-sale Securities, Debt Maturities, Fair Value, Fiscal Year Maturity [Abstract]	'	'
Due within one year	$127,081	'
After one but within five years	326,885	'
Total	$453,966	$916,223

Balance_Sheet_Account_Details_4

Balance Sheet Account Details (Details 3) (USD $)	Dec. 29, 2013	Dec. 30, 2012
In Thousands, unless otherwise specified
Accounts Receivable [Line Items]	'	'
Accounts receivable, gross	$242,626	$219,255
Allowance for doubtful accounts	-3,680	-4,280
Total accounts receivable, net	238,946	214,975
Accounts receivable from product and service sales [Member]	'	'
Accounts Receivable [Line Items]	'	'
Accounts receivable, gross	241,360	217,369
Other receivables [Member]	'	'
Accounts Receivable [Line Items]	'	'
Accounts receivable, gross	$1,266	$1,886

Balance_Sheet_Account_Details_5

Balance Sheet Account Details (Details 4) (USD $)	Dec. 29, 2013	Dec. 30, 2012
In Thousands, unless otherwise specified
Inventory [Abstract]	'	'
Raw materials	$57,398	$61,665
Work in process	70,016	75,675
Finished goods	26,685	21,378
Total inventory	$154,099	$158,718

Balance_Sheet_Account_Details_6

Balance Sheet Account Details (Details 5) (USD $)	Dec. 29, 2013	Dec. 30, 2012
In Thousands, unless otherwise specified
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	$380,167	$319,571
Accumulated depreciation	-177,501	-153,404
Total property and equipment, net	202,666	166,167
Leasehold improvements [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	104,571	87,734
Machinery and equipment [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	175,340	158,112
Computer hardware and software [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	73,544	58,313
Furniture and fixtures [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	10,511	8,022
Building [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	7,670	'
Construction in progress [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	$8,531	$7,390

Balance_Sheet_Account_Details_7

Balance Sheet Account Details (Details 6) (USD $)	12 Months Ended		15 Months Ended
In Thousands, unless otherwise specified	Dec. 30, 2012	Jan. 01, 2012	Dec. 30, 2012
Restructuring Cost and Reserve [Line Items]	'	'	'
Restructuring reserve, beginning of period	$3,526	'	'
Additional expenses	3,522	8,136	'
Cash Payments for Restructuring	-7,048	'	'
Restructuring reserve, end of period	0	3,526	0
Cumulative expense recorded since inception in restructuring expense	'	'	11,658
Employee Severance Separation Cost [Member]	'	'	'
Restructuring Cost and Reserve [Line Items]	'	'	'
Restructuring reserve, beginning of period	3,496	'	'
Additional expenses	2,780	'	'
Cash Payments for Restructuring	-6,276	'	'
Restructuring reserve, end of period	0	'	0
Cumulative expense recorded since inception in restructuring expense	'	'	10,463
Facilities Exit Costs [Member]	'	'	'
Restructuring Cost and Reserve [Line Items]	'	'	'
Restructuring reserve, beginning of period	0	'	'
Additional expenses	221	'	'
Cash Payments for Restructuring	-221	'	'
Restructuring reserve, end of period	0	'	0
Cumulative expense recorded since inception in restructuring expense	'	'	221
Other Restructuring Costs [Member]	'	'	'
Restructuring Cost and Reserve [Line Items]	'	'	'
Restructuring reserve, beginning of period	30	'	'
Additional expenses	521	'	'
Cash Payments for Restructuring	-551	'	'
Restructuring reserve, end of period	0	'	0
Cumulative expense recorded since inception in restructuring expense	'	'	$974

Balance_Sheet_Account_Details_8

Balance Sheet Account Details (Details 7) (USD $)	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012	Jan. 02, 2011
In Thousands, unless otherwise specified
Accrued Liabilities, Current [Abstract]	'	'	'	'
Accrued compensation expenses	$82,705	$59,864	'	'
Deferred revenue, current portion	50,834	55,817	'	'
Accrued taxes payable	30,435	23,021	'	'
Customer deposits	13,569	13,765	'	'
Reserve for product warranties	10,407	10,136	11,966	16,761
Acquisition related contingent consideration liability, current portion	6,719	9,490	'	'
Facility exit obligation, current portion	5,570	8,063	'	'
Unsettled short-term investment purchase	'	9,154	'	'
Other	18,881	12,567	'	'
Total accrued liabilities	$219,120	$201,877	'	'

Balance_Sheet_Account_Details_9

Balance Sheet Account Details (Details Textual) (USD $)	12 Months Ended
	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
	securities		employees
Balance Sheet Account Details [Line Items]	'	'	'
Number of available-for-sale securities in a gross unrealized loss position	111	'	'
Prior period reclassification in statements of cash flows	'	$235,000,000	$332,400,000
Cost-method investments in non-publicly traded company	22,100,000	56,300,000	'
Cost method investment related gain (loss)	-61,357,000	-45,911,000	'
Recovery of previously impaired note receivable	6,000,000	'	'
Accrued expenditures included in capital expenditures	'	'	5,900,000
Number of employees involuntarily terminated	'	'	200
Oxford Nanopore Technologies [Member] [Member]	'	'	'
Balance Sheet Account Details [Line Items]	'	'	'
Cost method investment related gain (loss)	-55,200,000	'	'
deCode [Member]	'	'	'
Balance Sheet Account Details [Line Items]	'	'	'
Cost method investment related gain (loss)	'	-48,600,000	'
Other Cost Method Investment [Member]	'	'	'
Balance Sheet Account Details [Line Items]	'	'	'
Cost method investment related gain (loss)	'	$2,700,000	'

Acquisitions_Details

Acquisitions (Details) (USD $)	Dec. 29, 2013	Dec. 30, 2012	Feb. 21, 2013
In Thousands, unless otherwise specified			Verinata [Member]
Business Acquisition [Line Items]	'	'	'
Cash and cash equivalents	'	'	$9,151
Accounts receivable	'	'	2,801
Inventory	'	'	1,110
Prepaid expenses and other current assets	'	'	979
Property and equipment	'	'	12,083
Other assets	'	'	978
Intangible assets	'	'	176,490
Goodwill	723,061	369,327	227,453
Accounts payable	'	'	-2,539
Accrued liabilities	'	'	-3,803
Lease financing obligation	'	'	-9,695
Deferred tax liability	'	'	-18,741
Total purchase price	'	'	$396,267

Acquisitions_Details_1

Acquisitions (Details 1) (USD $)	12 Months Ended				0 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 29, 2013	Dec. 29, 2013	Dec. 29, 2013	Feb. 21, 2013	Feb. 21, 2013	Feb. 21, 2013	Feb. 21, 2013
		Developed technology [Member]	Customer relationships [Member]	Trade name [Member]	Verinata [Member]	Verinata [Member]	Verinata [Member]	Verinata [Member]
						Developed technology [Member]	Customer relationships [Member]	Trade name [Member]
Acquired Finite-Lived Intangible Assets [Line Items]	'	'	'	'	'	'	'	'
Weighted average useful lives of intangible assets acquired in period (in years)	'	'12 years	'4 years	'2 years	'	'13 years	'5 years	'2 years
Fair Value	$271,135	$249,900	$7,990	$2,200	$176,490	$170,200	$4,690	$1,600

Acquisitions_Details_2

Acquisitions (Details 2) (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012
Business Combinations [Abstract]	'	'
Net revenues	$1,433,935	$1,161,241
Net income	$113,869	$92,645
Net income per share-basic (in dollars per share)	$0.91	$0.75
Net income per share-diluted (in dollars per share)	$0.81	$0.69

Acquisitions_Details_3

Acquisitions (Details 3) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Contingent compensation expense [Member]	'	'	'
Business Combination, Separately Recognized Transactions [Line Items]	'	'	'
Contingent compensation expense	$13,610	$9,151	$6,057
Contingent compensation expense [Member] | Research and development expense [Member]	'	'	'
Business Combination, Separately Recognized Transactions [Line Items]	'	'	'
Contingent compensation expense	544	3,419	4,799
Contingent compensation expense [Member] | Selling, general and administrative expense [Member]	'	'	'
Business Combination, Separately Recognized Transactions [Line Items]	'	'	'
Contingent compensation expense	13,066	5,732	1,258
IPR&D [Member] | Acquisition related expense (gain), net [Member]	'	'	'
Business Combination, Separately Recognized Transactions [Line Items]	'	'	'
IPR&D, included in acquisition related expense (gain), net	'	'	$5,425

Acquisitions_Details_Textual

Acquisitions (Details Textual) (USD $)

12 Months Ended

12 Months Ended

0 Months Ended

0 Months Ended

12 Months Ended

12 Months Ended

0 Months Ended

Dec. 29, 2013

Dec. 30, 2012

Jan. 01, 2012

Dec. 27, 2013

Dec. 29, 2013

Dec. 29, 2013

Dec. 29, 2013

Dec. 29, 2013

Dec. 29, 2013

Feb. 21, 2013

Feb. 21, 2013

Feb. 21, 2013

Feb. 21, 2013

Feb. 21, 2013

Dec. 29, 2013

Feb. 21, 2013

Feb. 21, 2013

Dec. 29, 2013

Dec. 29, 2013

Dec. 29, 2013

Sep. 19, 2012

Sep. 19, 2012

Sep. 19, 2012

Sep. 19, 2012

Sep. 19, 2012

Jan. 10, 2011

Jan. 10, 2011

Jan. 10, 2011

Jan. 10, 2011

Jan. 10, 2011

Jan. 10, 2011

Developed technologies [Member]

Customer relationships [Member]

Trade name [Member]

Minimum [Member]

Maximum [Member]

Verinata [Member]

Verinata [Member]

Verinata [Member]

Verinata [Member]

Verinata [Member]

Verinata [Member]

Verinata [Member]

Verinata [Member]

Verinata [Member]

Series of individually immaterial business acquisitions [Member]

Series of individually immaterial business acquisitions [Member]

BlueGnome [Member]

BlueGnome [Member]

BlueGnome [Member]

BlueGnome [Member]

BlueGnome [Member]

Epicentre [Member]

Epicentre [Member]

Epicentre [Member]

Epicentre [Member]

Epicentre [Member]

Epicentre [Member]

Developed technologies [Member]

Customer relationships [Member]

Trade name [Member]

Building [Member]

Building [Member]

Minimum [Member]

Maximum [Member]

Transaction costs [Member]

Developed technologies [Member]

Developed technologies [Member]

Customer relationships [Member]

Trade name [Member]

Contingent compensation expense [Member]

Non-revenue based milestones [Member]

Revenue based milestones [Member]

Developed technologies [Member]

Customer relationships [Member]

Trade name [Member]

Acquisition related expense (gain), net [Member]

Maximum [Member]

Business Acquisition [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Business acquisition contract price

'

'

'

'

'

'

'

'

'

$350,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Contingent consideration payments, maximum

'

'

'

'

'

'

'

'

'

100,000,000

'

'

'

'

'

'

'

'

'

'

20,000,000

'

'

'

'

15,000,000

'

'

'

'

'

Business acquisition total consideration

'

'

'

'

'

'

'

'

'

396,300,000

'

'

'

'

'

'

'

'

'

'

95,500,000

'

'

'

'

71,400,000

'

'

'

'

'

Business acquisition net cash consideration

'

'

'

'

'

'

'

'

'

339,300,000

'

'

'

'

'

'

'

'

'

'

88,000,000

'

'

'

'

59,400,000

'

'

'

'

'

Fair value of contingent consideration to be settled in cash

'

'

'

'

'

'

'

'

'

56,200,000

'

'

'

'

'

'

'

'

'

'

7,500,000

'

'

'

'

'

4,600,000

7,400,000

'

'

'

Fair value of converted stock options

'

'

'

'

'

'

'

'

'

200,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Loss realized on settlement of preexisting relationships

'

'

'

'

'

'

'

'

'

500,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amount deposited in escrow

'

'

'

'

'

'

'

'

'

30,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Escrow period

'

'

'

'

'

'

'

'

'

'1 year 6 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Separately recognized transaction

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3,400,000

'

'

'

'

'

'

20,000,000

'

'

'

'

'

'

Number of unvested stock options to purchase Illumina stock

512,000

251,000

1,399,000

'

'

'

'

'

'

400,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Fair value of converted options

'

'

'

'

'

'

'

'

'

18,900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Share price (in dollars per share)

'

'

'

$110.38

'

'

'

'

'

$48.36

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Expected life

'

'

'

'

'

'

'

'

'

'2 years 4 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Weighted average risk free interest rate

'

'

'

'

'

'

'

'

'

0.32%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Weighted average annualized volatility

'

'

'

'

'

'

'

'

'

42.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Expected dividend yield

0.00%

'

'

'

'

'

'

'

'

0.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Weighted average grant date fair value (in dollars per share)

'

'

'

'

'

'

'

'

'

$42.63

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Discount rate for assessment of the acquisition date fair value

'

'

'

'

'

'

'

'

'

'

'

'

'

6.00%

'

6.00%

20.00%

'

'

'

30.00%

'

'

'

'

21.00%

'

'

'

'

'

Expected volatility rate

'

'

'

'

'

'

'

'

'

50.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Risk free interest rate

'

'

'

'

'

'

'

'

'

0.26%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Useful life

'

'

'

'

'

'

'

'3 years

'7 years

'

'

'

'

'30 years

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Future annual minimum payments due

'

'

'

'

'

'

'

'

'

'

'

'

'

900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Future minimum payments due in 2017

'

'

'

'

'

'

'

'

'

'

'

'

'

'

8,300,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Goodwill

723,061,000

369,327,000

'

'

'

'

'

'

'

227,453,000

'

'

'

'

'

'

'

'

126,300,000

'

47,500,000

'

'

'

'

43,600,000

'

'

'

'

'

Consideration to identified intangible assets

'

'

'

'

'

'

'

'

'

176,490,000

'

'

'

'

'

'

'

'

'

79,700,000

'

25,000,000

16,800,000

7,100,000

'

26,900,000

'

'

23,300,000

1,100,000

2,500,000

Weighted average useful life of identified intangible assets

'

'

'

'

'12 years

'4 years

'2 years

'

'

'

'13 years

'5 years

'2 years

'

'

'

'

'

'

'8 years

'

'7 years

'5 years

'10 years

'

'

'

'

'9 years

'3 years

'10 years

Share issued to shareholders in connection with business acquisition

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

229,000

'

'

'

'

'

Portion of shares issued determined to be part of the purchase price

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

33.33%

'

'

'

'

'

Total consideration to tangible assets, net of liabilities

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$900,000

'

'

'

'

'

Intangible_Assets_Details

Intangible Assets (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012
Intangible asset, gross carrying amount	$427,548	$189,913
Accumulated amortization	-96,375	-59,717
Intangible assets, net	331,173	130,196
Intangible assets acquired, gross carrying amount	271,135	'
Intangible Assets With Finite Useful Lives, Future Amortization Expense [Abstract]	'	'
2014	49,376	'
2015	45,974	'
2016	40,582	'
2017	36,106	'
2018	27,310	'
Thereafter	131,825	'
Total	331,173	'
Licensed technologies [Member]	'	'
Intangible asset, gross carrying amount	48,361	47,329
Accumulated amortization	-31,927	-25,471
Intangible assets, net	16,434	21,858
Weighted average useful lives of intangible assets acquired in period (in years)	'5 years	'
Intangible assets acquired, gross carrying amount	1,032	'
Core technologies [Member]	'	'
Intangible asset, gross carrying amount	321,700	99,800
Accumulated amortization	-45,534	-27,427
Intangible assets, net	276,166	72,373
Weighted average useful lives of intangible assets acquired in period (in years)	'12 years	'
Intangible assets acquired, gross carrying amount	249,900	'
Customer relationships [Member]	'	'
Intangible asset, gross carrying amount	26,770	18,780
Accumulated amortization	-7,376	-2,214
Intangible assets, net	19,394	16,566
Weighted average useful lives of intangible assets acquired in period (in years)	'4 years	'
Intangible assets acquired, gross carrying amount	7,990	'
License agreements [Member]	'	'
Intangible asset, gross carrying amount	18,917	14,404
Accumulated amortization	-4,947	-3,933
Intangible assets, net	13,970	10,471
Weighted average useful lives of intangible assets acquired in period (in years)	'10 years	'
Intangible assets acquired, gross carrying amount	10,013	'
Trade Names [Member]	'	'
Intangible asset, gross carrying amount	11,800	9,600
Accumulated amortization	-6,591	-672
Intangible assets, net	5,209	8,928
Weighted average useful lives of intangible assets acquired in period (in years)	'2 years	'
Intangible assets acquired, gross carrying amount	$2,200	'

Fair_Value_Measurement_Details

Fair Value Measurement (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Change in estimated fair value of the contingent consideration liability	'	'	'
Change in estimated fair value, recorded in acquisition related (gain) expense, net	($18,784)	$1,975	($4,500)
Level 3 [Member]	'	'	'
Liability:	'	'	'
Acquisition related contingent consideration liabilities	49,480	12,519	6,638
Change in estimated fair value of the contingent consideration liability	'	'	'
Balance as of beginning of period	12,519	6,638	3,738
Additional liability recorded for acquisitions	60,184	'	'
Change in estimated fair value, recorded in acquisition related (gain) expense, net	-18,784	1,975	-4,500
Cash payments	-4,439	-3,594	'
Balance as of end of period	49,480	12,519	6,638
Level 3 [Member] | Epicentre [Member]	'	'	'
Change in estimated fair value of the contingent consideration liability	'	'	'
Additional liability recorded for acquisitions	'	'	7,400
Level 3 [Member] | BlueGnome [Member]	'	'	'
Change in estimated fair value of the contingent consideration liability	'	'	'
Additional liability recorded for acquisitions	'	7,500	'
Fair Value, Measurements, Recurring [Member]	'	'	'
Assets:	'	'	'
Money market funds (cash equivalent)	478,755	252,126	'
Deferred compensation plan assets	17,805	13,626	'
Total assets measured at fair value	950,526	1,181,975	'
Liability:	'	'	'
Acquisition related contingent consideration liabilities	49,480	12,519	'
Deferred compensation liability	14,957	12,071	'
Total liabilities measured at fair value	64,437	24,590	'
Change in estimated fair value of the contingent consideration liability	'	'	'
Balance as of end of period	49,480	12,519	'
Fair Value, Measurements, Recurring [Member] | Debt securities in government sponsored entities [Member]	'	'	'
Assets:	'	'	'
Investments, fair value disclosure	82,143	314,873	'
Fair Value, Measurements, Recurring [Member] | Corporate debt securities [Member]	'	'	'
Assets:	'	'	'
Investments, fair value disclosure	341,970	472,861	'
Fair Value, Measurements, Recurring [Member] | U.S. Treasury securities [Member]	'	'	'
Assets:	'	'	'
Investments, fair value disclosure	29,853	128,489	'
Fair Value, Measurements, Recurring [Member] | Level 1 [Member]	'	'	'
Assets:	'	'	'
Money market funds (cash equivalent)	478,755	252,126	'
Total assets measured at fair value	508,608	380,615	'
Fair Value, Measurements, Recurring [Member] | Level 1 [Member] | U.S. Treasury securities [Member]	'	'	'
Assets:	'	'	'
Investments, fair value disclosure	29,853	128,489	'
Fair Value, Measurements, Recurring [Member] | Level 2 [Member]	'	'	'
Assets:	'	'	'
Deferred compensation plan assets	17,805	13,626	'
Total assets measured at fair value	441,918	801,360	'
Liability:	'	'	'
Deferred compensation liability	14,957	12,071	'
Total liabilities measured at fair value	14,957	12,071	'
Fair Value, Measurements, Recurring [Member] | Level 2 [Member] | Debt securities in government sponsored entities [Member]	'	'	'
Assets:	'	'	'
Investments, fair value disclosure	82,143	314,873	'
Fair Value, Measurements, Recurring [Member] | Level 2 [Member] | Corporate debt securities [Member]	'	'	'
Assets:	'	'	'
Investments, fair value disclosure	341,970	472,861	'
Fair Value, Measurements, Recurring [Member] | Level 3 [Member]	'	'	'
Liability:	'	'	'
Acquisition related contingent consideration liabilities	49,480	12,519	'
Total liabilities measured at fair value	49,480	12,519	'
Change in estimated fair value of the contingent consideration liability	'	'	'
Balance as of end of period	$49,480	$12,519	'

Convertible_Senior_Notes_Detai

Convertible Senior Notes (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Jan. 01, 2012
Extinguishment of Debt [Line Items]	'	'
Loss on extinguishment of debt	($555)	($37,611)
Convertible Senior Notes due Two Zero One Four [Member]	'	'
Extinguishment of Debt [Line Items]	'	'
Cash paid for principal of notes converted	10,555	'
Conversion value over principal amount paid in shares of common stock	21,217	'
Number of shares of common stock issued upon conversion	317	'
Loss on extinguishment of debt	$555	'
Minimum [Member] | Convertible Senior Notes due Two Zero One Four [Member]	'	'
Extinguishment of Debt [Line Items]	'	'
Effective interest rate used to measure fair value of converted notes upon conversion	0.50%	'
Maximum [Member] | Convertible Senior Notes due Two Zero One Four [Member]	'	'
Extinguishment of Debt [Line Items]	'	'
Effective interest rate used to measure fair value of converted notes upon conversion	0.80%	'

Convertible_Senior_Notes_Detai1

Convertible Senior Notes (Details 1) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Dec. 29, 2013	Jan. 01, 2012
			2014 Notes [Member]	2016 Notes [Member]
Summarized information about equity and liability components of convertible senior notes	'	'	'	'
Principal amount of convertible notes outstanding	$949,570	$960,125	$29,600	'
Unamortized discount of liability component	-80,977	-117,752	'	'
Net carrying amount of liability component	868,593	842,373	'	'
Less: current portion	-29,288	-36,967	'	'
Long-term debt	839,305	805,406	'	'
Conversion option subject to cash settlement	282	3,158	'	'
Carrying value of equity component, net of debt issuance cost	274,304	271,966	'	155,400
Fair value of outstanding notes	$1,428,743	$993,916	'	'
Weighted average remaining amortization period of discount on the liability component	'2 years	'3 years	'	'

Convertible_Senior_Notes_Detai2

Convertible Senior Notes (Details Textual) (USD $)	Dec. 29, 2013	Dec. 30, 2012	Dec. 29, 2013	Jan. 01, 2012	Dec. 29, 2013	Dec. 30, 2007	Dec. 30, 2007
Share data in Millions, except Per Share data, unless otherwise specified			2016 Notes [Member]	2016 Notes [Member]	2014 Notes [Member]	2014 Notes [Member]	Warrant [Member]
							2014 Notes [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 issuance price as a percentage of principal	'	'	'	98.25%	'	'	'
Debt issuance costs	'	'	'	400,000	'	'	'
Amortization period for debt issuance cost	'	'	'	'5 years	'	'	'
Conversion rate per 1,000 principal amount of notes	'	'	'	11.9687	'	'	'
Principal amount used in calculating incremental share settlement amount	'	'	'	1,000	'	'	'
Conversion Price	'	'	'	$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 business days 2016 notes are convertible after measurement period	'	'	'	'20 days	'	'	'
Number of consecutive trading days in the measurement period	'	'	'	'20 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	'	'	'	'20 or more	'	'	'
Number of consecutive trading days on which trading price is examined for triggering of conversion	'	'	'	'30 days	'	'	'
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%	'	'	'
Maximum payment on principal portion to be cash settled upon conversion	'	'	'	1,000	'	'	'
Debt Instrument, Maturity Date	'	'	'	15-Mar-16	'	15-Feb-14	'
Repurchase Price as a Percentage of Principal Amount upon designated events	'	'	'	100.00%	'	'	'
Effective interest rate used to measure fair value of convertible senior note	'	'	'	4.50%	'	8.30%	'
Fair value of liability component at issuance	'	'	'	748,500,000	'	'	'
Carrying value of equity component, net of debt issuance cost	274,304,000	271,966,000	'	155,400,000	'	'	'
Cash proceeds	'	'	'	903,900,000	'	'	'
If-converted value in excess of principal	'	'	209,000,000	'	109,300,000	'	'
Maximum Shares Entitles to Purchase Shares Under Hedge Transaction Upon Issuance of Convertible Senior Notes	'	'	'	'	'	18.3	'
Strike price under hedge transaction upon issuance of the convertible senior notes	'	'	'	'	'	$21.83	'
Class of Warrant or Right, Outstanding	'	'	'	'	'	'	18.3
Class of Warrant or Right, Exercise Price of Warrants or Rights1	$31.43	'	'	'	'	'	$31.43
Principal amount of convertible notes outstanding	$949,570,000	$960,125,000	'	'	$29,600,000	'	'
Maximum shares entitles to purchase shares under hedge transaction upon issuance of convertible senior notes outstanding principal	'	'	'	'	1.4	'	'

Commitments_Details

Commitments (Details) (USD $)	Dec. 29, 2013
In Thousands, unless otherwise specified
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]	'
Operating lease, current - 2014	$29,526
Operating lease, due in two years - 2015	29,463
Operating lease, due in three years - 2016	29,327
Operating lease, due in four years - 2017	29,383
Operating lease, due in five years - 2018	29,601
Operating lease, due after five years - Thereafter	395,342
Operating lease, total future minimum payments due	542,642
Sublease, current - 2104	-2,478
Sublease, receivable in two years - 2015	-2,552
Sublease, receivable in three years - 2016	-2,629
Sublease, receivable in four years - 2017	-2,708
Sublease, receivable in five years - 2018	-2,789
Sublease, receivable after five years - Thereafter	-14,708
Sublease, total future minimum receivable	-27,864
Operating leases, net - current - 2014	27,048
Operating lease, net, due in two years - 2105	26,911
Operating lease, net, due in three years - 2106	26,698
Operating lease, net, due in four years - 2017	26,675
Operating lease, net, due in five years - 2018	26,812
Operating lease, net, due after five years - Thereafter	380,634
Operating lease, total net future minimum payments due	$514,778

Commitments_Details_1

Commitments (Details 1) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012
Commitments and Contingencies Disclosure [Abstract]	'	'
Headquarters facility exit obligation balance, beginning of period	$45,352	$25,049
Adjustment to facility exit obligation	-114	24,878
Accretion of interest expense	2,738	2,129
Cash payments	-9,758	-6,704
Heaqdquarters facility exit obligation balance, end of period	$38,218	$45,352

Commitments_Details_2

Commitments (Details 2) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Reserve for product warranties	'	'	'
Balance as of beginning of period	$10,136	$11,966	$16,761
Additions charged to cost of revenue	15,674	17,279	17,913
Repairs and replacements	-15,403	-19,109	-22,708
Balance as of end of period	$10,407	$10,136	$11,966

Commitments_Details_Textual

Commitments (Details Textual) (USD $)	12 Months Ended
	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Commitments and Contingencies Disclosure [Abstract]	'	'	'
Lease Expiration Date	'2031	'	'
Number of lease renewal options	4	'	'
Lease renewal option term	'5 years	'	'
Initial sublease term for former headquarters	'10 years	'	'
Initial letter of credit amount	$8,000,000	'	'
Letters of credit amount at end of lease term	0	'	'
Rent expense	$28,100,000	$21,400,000	$17,400,000

Sharebased_Compensation_Expens2

Share-based Compensation Expense (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Share-based Compensation	'	'	'
Share-based compensation expense before taxes	$105,826	$94,324	$92,092
Related income tax benefits	-32,819	-30,759	-32,168
Share-based compensation expense, net of taxes	73,007	63,565	59,924
Cost of product revenue [Member]	'	'	'
Share-based Compensation	'	'	'
Share-based compensation expense before taxes	6,223	7,575	6,951
Cost of service and other revenue [Member]	'	'	'
Share-based Compensation	'	'	'
Share-based compensation expense before taxes	777	461	695
Research and development [Member]	'	'	'
Share-based Compensation	'	'	'
Share-based compensation expense before taxes	37,439	30,879	32,105
Selling, general and administrative [Member]	'	'	'
Share-based Compensation	'	'	'
Share-based compensation expense before taxes	$61,387	$55,409	$52,341

Sharebased_Compensation_Expens3

Share-based Compensation Expense (Details 1) (USD $)	12 Months Ended
	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012	Jan. 02, 2011
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'	'	'	'
Expected dividend yield	0.00%	'	'	'
Stock Options [Member]	'	'	'	'
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'	'	'	'
Interest rate, minimum	0.14%	0.56%	0.85%	'
Interest rate, maximum	1.86%	0.93%	2.23%	'
Volatility, minimum	30.00%	41.00%	41.00%	'
Volatility, maximum	44.00%	48.00%	53.00%	'
Expected dividend yield	0.00%	0.00%	0.00%	'
Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Weighted Average Grant Date Fair Value	$40.66	$15.47	$27.47	'
Stock Options [Member] | Maximum [Member]	'	'	'	'
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'	'	'	'
Expected life	'9 years 5 months	'6 years 7 months	'5 years 6 months	'
Stock Options [Member] | Minimum [Member]	'	'	'	'
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'	'	'	'
Expected life	'0 years 9 months	'4 years	'4 years 8 months	'
Employee Stock Purchase Rights [Member]	'	'	'	'
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'	'	'	'
Interest rate, minimum	0.08%	0.09%	0.16%	'
Interest rate, maximum	0.15%	0.17%	0.30%	'
Volatility, minimum	31.00%	33.00%	43.00%	'
Volatility, maximum	32.00%	64.00%	48.00%	'
Expected dividend yield	0.00%	0.00%	'	0.00%
Weighted Average Grant Date Fair Value per Share, Awarded	$19.30	$16.45	$20.08	'
Employee Stock Purchase Rights [Member] | Maximum [Member]	'	'	'	'
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'	'	'	'
Expected life	'1 year	'1 year	'1 year	'
Employee Stock Purchase Rights [Member] | Minimum [Member]	'	'	'	'
Assumptions used to estimate the fair value per share of options granted and employee stock purchase rights granted	'	'	'	'
Expected life	'6 months	'6 months	'6 months	'

Sharebased_Compensation_Expens4

Share-based Compensation Expense (Details Textual) (USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 29, 2013
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	$216.90
Weighted-average period of unrecognized compensation cost related to stock options, restricted stock, and ESPP shares issued to date	'2 years 2 months

Stockholders_Equity_Details

Stockholders' Equity (Details) (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Options	'	'	'
Options, Outstanding at Period Start	8,351	10,378	11,882
Options, Granted	512	251	1,399
Options, Exercised	-3,006	-2,071	-2,784
Options, Cancelled	-133	-207	-119
Options, Outstanding at Period End	5,724	8,351	10,378
Weighted-Average Exercise Price	'	'	'
Weighted-Average Exercise Price, Outstanding at Period Start (in dollars per share)	$32.10	$29.69	$22.83
Weighted Average Exercise Price, Granted (in dollars per share)	$14.74	$40.79	$64.98
Weighted Average Exercise Price, Exercised (in dollars per share)	$27.70	$20.34	$17.98
Weighted Average Exercise Price, Cancelled (in dollars per share)	$41.80	$39.18	$33.49
Weighted-Average Exercise Price, Outstanding at Period End (in dollars per share)	$32.64	$32.10	$29.69

Stockholders_Equity_Details_1

Stockholders' Equity (Details 1) (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Restricted Stock Awards [Member]	'	'	'
Restricted stock	'	'	'
Restricted Stock, Outstanding at Period Start	465	230	'
Restricted Stock, Awarded	'	312	230
Restricted Stock, Vested	-217	-77	'
Restricted Stock, Outstanding at Period End	248	465	230
Weighted Average Grant-Date Fair Value per Share	'	'	'
Weighted Average Grant Date Fair Value per Share, Outstanding at Period Start (in dollars per share)	$53.84	$65.95	'
Weighted Average Grant Date Fair Value per Share, Awarded (in dollars per share)	'	$47.91	$65.95
Weighted Average Grant Date Fair Value per Share, Vested (in dollars per share)	$54.27	$65.95	'
Weighted Average Grant Date Fair Value per Share, Outstanding at Period End (in dollars per share)	$53.46	$53.84	$65.95
Restricted Stock Units [Member]	'	'	'
Restricted stock	'	'	'
Restricted Stock, Outstanding at Period Start	3,660	3,476	3,109
Restricted Stock, Awarded	1,532	1,640	1,550
Restricted Stock, Vested	-1,308	-1,062	-827
Restricted Stock, Cancelled	-256	-394	-356
Restricted Stock, Outstanding at Period End	3,628	3,660	3,476
Weighted Average Grant-Date Fair Value per Share	'	'	'
Weighted Average Grant Date Fair Value per Share, Outstanding at Period Start (in dollars per share)	$45.49	$41.87	$40.39
Weighted Average Grant Date Fair Value per Share, Awarded (in dollars per share)	$77.53	$48.52	$42.02
Weighted Average Grant Date Fair Value per Share, Vested (in dollars per share)	$42.97	$38.48	$36.47
Weighted Average Grant Date Fair Value per Share, Cancelled (in dollars per share)	$49.24	$45.05	$42.15
Weighted Average Grant Date Fair Value per Share, Outstanding at Period End (in dollars per share)	$59.66	$45.49	$41.87
Performance Stock Units [Member]	'	'	'
Restricted stock	'	'	'
Restricted Stock, Outstanding at Period Start	587	'	'
Restricted Stock, Awarded	584	599	'
Restricted Stock, Cancelled	-70	-12	'
Restricted Stock, Outstanding at Period End	1,101	587	'
Weighted Average Grant-Date Fair Value per Share	'	'	'
Weighted Average Grant Date Fair Value per Share, Outstanding at Period Start (in dollars per share)	$49.64	'	'
Weighted Average Grant Date Fair Value per Share, Awarded (in dollars per share)	$59.16	$49.66	'
Weighted Average Grant Date Fair Value per Share, Cancelled (in dollars per share)	$50.42	$50.54	'
Weighted Average Grant Date Fair Value per Share, Outstanding at Period End (in dollars per share)	$54.64	$49.64	'

Stockholders_Equity_Details_2

Stockholders' Equity (Details 2) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Restricted Stock Awards [Member]	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'
Pre-tax intrinsic value of outstanding restricted and performance stock	$27,384	$25,437	$6,986
Fair value of restricted and performance stock vested	11,750	5,039	'
Restricted Stock Units [Member]	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'
Pre-tax intrinsic value of outstanding restricted and performance stock	400,421	200,383	105,944
Fair value of restricted and performance stock vested	56,212	40,870	30,155
Performance Shares Units [Member]	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'
Pre-tax intrinsic value of outstanding restricted and performance stock	$121,555	$32,149	'

Stockholders_Equity_Details_Te

Stockholders' Equity (Details Textual) (USD $)

1 Months Ended

12 Months Ended

0 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

12 Months Ended

12 Months Ended

Jul. 28, 2013

Dec. 29, 2013

Dec. 30, 2012

Jan. 01, 2012

Dec. 27, 2013

Dec. 30, 2007

Apr. 18, 2013

Jan. 30, 2014

Aug. 31, 2011

Jan. 01, 2012

Jul. 31, 2010

Jan. 01, 2012

Dec. 29, 2013

Dec. 29, 2013

Dec. 29, 2013

Dec. 29, 2013

Dec. 29, 2013

Dec. 29, 2013

16-May-14

Dec. 29, 2013

Dec. 29, 2013

Dec. 29, 2013

Dec. 30, 2012

Jan. 01, 2012

Jan. 25, 2012

Jan. 25, 2012

Jan. 25, 2012

April 18, 2012 Discretionary Plan [Member]

January 30 2014 Stock Repurchase Program [Member]

August 2011 Discretionary Plan [Member]

Discretionary Repurchase Concurrent with 2016 Note Issuance [Member]

July 2010 Repurchase Program [Member]

July 2010 Repurchase Program [Member]

Stock Options [Member]

Stock Options [Member]

Restricted Stock Units [Member]

Performance Stock Units [Member]

Performance Stock Units [Member]

Performance Stock Units [Member]

Warrant [Member]

2005 Stock Plan [Member]

2005 Illumina, 2005 Solexa, and 2008 Verinata Stock Plan [Member]

Employee Stock Purchase Plan [Member]

Employee Stock Purchase Plan [Member]

Employee Stock Purchase Plan [Member]

Stockholder Rights Plan [Member]

Stockholder Rights Plan [Member]

Stockholder Rights Plan [Member]

Minimum [Member]

Maximum [Member]

Minimum [Member]

Maximum [Member]

Minimum [Member]

Maximum [Member]

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

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Increase in the maximum number of shares of common stock authorized for issuance (in shares)

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5,000,000

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Shares available for issuance

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'

'

6,800,000

15,000,000

15,400,000

'

'

'

'

Vesting period

'

'

'

'

'

'

'

'

'

'

'

'

'4 years

'5 years

'4 years

'

'

'

'

'

'

'

'

'

'

'

'

Percentage of options vesting on the first anniversary of the grant date

'

'

'

'

'

'

'

'

'

'

'

'

20.00%

25.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

Maximum term of each grant of options

'

'

'

'

'

'

'

'

'

'

'

'

'

'10 years

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock options exercisable (in shares)

'

4,700,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock options exercisable outstanding weighted average exercise price per share (in dollars per share)

'

$31.83

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Weighted average remaining life in years of options outstanding

'

'4 years 11 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Weighted average remaining life in years of options exercisable

'

'4 years 6 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Aggregate intrinsic value of options outstanding

'

$445,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Aggregate intrinsic value of options exercisable

'

370,900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Share price (in dollars per share)

'

'

'

'

$110.38

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Total intrinsic value of options exercised

'

141,700,000

60,600,000

136,500,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Total fair value of options vested

'

24,000,000

31,900,000

49,500,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Vesting percentage, 1st anniversary

'

'

'

'

'

'

'

'

'

'

'

'

'

'

15.00%

'

'

'

'

'

'

'

'

'

'

'

'

Vesting percentage, 2nd anniversary

'

'

'

'

'

'

'

'

'

'

'

'

'

'

20.00%

'

'

'

'

'

'

'

'

'

'

'

'

Vesting percentage, 3rd anniversary

'

'

'

'

'

'

'

'

'

'

'

'

'

'

30.00%

'

'

'

'

'

'

'

'

'

'

'

'

Vesting percentage, 4th anniversary

'

'

'

'

'

'

'

'

'

'

'

'

'

'

35.00%

'

'

'

'

'

'

'

'

'

'

'

'

Performance stock award performance period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'3 years

'

'

'

'

'

'

'

'

'

'

'

Percentage of shares approved issuable at end of performance period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

50.00%

150.00%

'

'

'

'

'

'

'

'

'

ESPP Number of shares authorized

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

15,500,000

'

'

'

'

'

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%

'

'

'

'

'

Annual percent increases of shares available for issuance

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3.00%

'

'

'

'

'

ESPP Annual increases of shares available for issuance

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3,000,000

'

'

'

'

'

Total shares issued under the ESPP

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

400,000

328,000

328,000

'

'

'

Exercise price of warrants held by hedging counter parties (in dollars per share)

'

$31.43

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of common shares callable by warrants settled in period

3,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of common shares called by warrants

'

15,400,000

'

'

'

18,300,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Warrant Expiration Period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'40 days

'

'

'

'

'

'

'

'

Number of shares purchased for warrants exercised

'

'

'

505,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

(Payments for) proceeds from warrant settlements

-125,000,000

-125,000,000

'

5,512,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Repurchase of common shares (in shares)

'

900,000

1,900,000

'

'

'

'

'

'

4,900,000

'

2,400,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Common stock repurchases (in dollars)

'

50,020,000

82,522,000

570,406,000

'

'

'

'

'

314,300,000

'

156,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock repurchase program authorized amount

'

'

'

'

'

'

250,000,000

250,000,000

100,000,000

'

200,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Dollar amount remaining in authorized stock repurchase program

'

117,500,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Allocated to repurchasing company common stock under a 10b5-1 plan

'

'

'

'

'

'

'

'

'

'

100,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Period in force for repurchases under 10b5-1 plan

'

'

'

'

'

'

'

'

'

'

'12 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amount allocated to repurchasing Company common stock during open trading windows

'

'

'

'

'

'

'

'

'

'

$100,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Preferred stock, par value (in dollars per share)

'

$0.01

$0.01

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$0.01

'

'

Dividend price per share of Series A Junior Participating Preferred Stock (in dollars per Right)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

275

'

'

Dividend portion of a share of Series A Junior Participating Preferred Stock

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

0.001

'

'

Minimum percent ownership of outstanding common stock required to exercise rights

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

15.00%

'

'

Price per right Board of Directors are entitled to redeem rights (in dollars per Right)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

0.001

'

'

Number of shares per Right

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1

'

'

Percent ownership of outstanding common stock required prior to exchange by board of directors

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

15.00%

50.00%

Legal_Proceedings_Legal_Procee

Legal Proceedings Legal Proceedings (Details Textual) (USD $)	0 Months Ended
	Jul. 02, 2013	Dec. 29, 2013
Loss Contingencies [Line Items]	'	'
Final Amended Judgment amount	$115,100,000	'
Final Amended Judgment royalty rate	8.00%	'
Long-term legal contingencies	'	132,933,000
Syntrix [Member]	'	'
Loss Contingencies [Line Items]	'	'
Long-term legal contingencies	'	132,900,000
Ongoing royalty amount deposited with the Court	'	12,000,000
Operating Expense [Member] | Syntrix [Member]	'	'
Loss Contingencies [Line Items]	'	'
Long-term legal contingencies	'	$114,600,000

Income_Taxes_Details

Income Taxes (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Income Tax Disclosure [Abstract]	'	'	'
United States	($53,703)	$102,296	($7,100)
Foreign	213,017	120,312	140,145
Income before income taxes	$159,314	$222,608	$133,045

Income_Taxes_Details_1

Income Taxes (Details 1) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Current:	'	'	'
Federal	$78,419	$57,285	$43,161
State	8,854	10,121	3,958
Foreign	39,416	31,504	24,154
Total current provision	126,689	98,910	71,273
Deferred:	'	'	'
Federal	-69,102	-7,724	-22,738
State	-15,222	-7,708	-8,050
Foreign	-8,359	-12,124	5,932
Total deferred benefit	-92,683	-27,556	-24,856
Total tax provision	$34,006	$71,354	$46,417

Income_Taxes_Details_2

Income Taxes (Details 2) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Income Tax Disclosure [Abstract]	'	'	'
Tax at federal statutory rate	$55,760	$77,913	$46,566
State, net of federal benefit	647	4,056	-49
Research and other credits	-10,977	-2,613	-7,418
Acquired in-process research & development	'	137	1,989
Change in valuation allowance	10,544	-37	-688
Permanent differences	1,120	2,380	1,668
Change in fair value of contingent consideration	-3,859	'	-1,311
Impact of foreign operations	-18,006	-11,470	5,579
Other	-1,223	988	81
Total tax provision	$34,006	$71,354	$46,417

Income_Taxes_Details_3

Income Taxes (Details 3) (USD $)	Dec. 29, 2013	Dec. 30, 2012
In Thousands, unless otherwise specified
Deferred tax assets:	'	'
Net operating losses	$66,969	$2,564
Tax credits	36,277	16,447
Other accruals and reserves	103,539	47,306
Stock compensation	36,728	39,175
Inventory adjustments	9,034	8,977
Impairment of cost-method investment	3,540	1,406
Other amortization	9,571	5,195
Other	14,704	13,469
Total gross deferred tax assets	280,362	134,539
Valuation allowance on deferred tax assets	-19,132	-1,756
Total deferred tax assets	261,230	132,783
Deferred tax liabilities:	'	'
Purchased intangible amortization	-98,671	-20,116
Convertible debt	-27,821	-38,910
Property and equipment	-13,311	-10,867
Other	-6,349	-6,682
Total deferred tax liabilities	-146,152	-76,575
Net deferred tax assets	$115,078	$56,208

Income_Taxes_Details_4

Income Taxes (Details 4) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Reconciliation of Unrecognized Tax Benefits, Excluding Amounts Pertaining to Examined Tax Returns [Roll Forward]	'	'	'
Balance at beginning of year	$37,585	$28,396	$22,729
Increases related to prior year tax positions	4,794	2,573	875
Decreases related to prior year tax positions	-223	-69	-382
Increases related to current year tax positions	7,503	6,685	5,174
Decreases related to lapse of statute of limitations	-613	'	'
Balance at end of year	$49,046	$37,585	$28,396

Income_Taxes_Details_Textual

Income Taxes (Details Textual) (USD $)	12 Months Ended
	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Income Taxes [Line Items]	'	'	'
Valuation allowance	$19,132,000	$1,756,000	'
Change in deferred tax asset valuation related to limitation of foreign tax credit	17,400,000	'	'
Change in valuation allowance	10,544,000	-37,000	-688,000
Deferred tax asset related to current period acquisition goodwill	6,800,000	'	'
Excess tax benefits realized	53,032,000	17,015,000	43,122,000
Unrealized excess tax benefits associated with share-based compensation	3,600,000	'	'
Decrease to the provision for income taxes	7,500,000	'	'
Increase to net income per diluted share	$0.05	'	'
Undistributed earnings of foreign subsidiaries	235,100,000	'	'
Uncertain tax positions that would reduce annual effective tax rate, if recognized	40,100,000	29,900,000	'
Potential interest penalties on uncertain tax positions	1,000,000	800,000	1,100,000
Liability recorded for potential interest and penalties	3,500,000	2,100,000	'
Federal [Domain]	'	'	'
Income Taxes [Line Items]	'	'	'
Net operating loss carryforwards	164,200,000	'	'
Research and development tax credit carryforwards	16,100,000	'	'
State [Member]	'	'	'
Income Taxes [Line Items]	'	'	'
Net operating loss carryforwards	228,100,000	'	'
Research and development tax credit carryforwards	$51,500,000	'	'

Employee_Benefit_Plans_Details

Employee Benefit Plans (Details Textual) (USD $)	12 Months Ended
	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Matching contributions	$7,000,000	$5,500,000	$5,300,000
Percent of base salary available for contribution to the deferred compensation plan	80.00%	'	'
Percent of all other forms of compensation available for contribution to the deferred compensation plan	100.00%	'	'
Fair Value, Measurements, Recurring [Member]	'	'	'
Assets of the Deferred Compensation Plan rabbi trust	17,805,000	13,626,000	'
Liabilities of the Deferred Compensation Plan rabbi trust	14,957,000	12,071,000	'
Fair Value, Measurements, Recurring [Member] | Level 2 [Member]	'	'	'
Assets of the Deferred Compensation Plan rabbi trust	17,805,000	13,626,000	'
Liabilities of the Deferred Compensation Plan rabbi trust	$14,957,000	$12,071,000	'

Segment_Information_Geographic2

Segment Information, Geographic Data, and Significant Customers (Details) (USD $)	3 Months Ended								12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013	Sep. 29, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 30, 2012	Sep. 30, 2012	Jul. 01, 2012	Apr. 01, 2012	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Revenue	$387,326	$356,800	$346,094	$330,958	$309,265	$285,874	$280,607	$272,770	$1,421,178	$1,148,516	$1,055,535
United States [Member]	'	'	'	'	'	'	'	'	'	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Revenue	'	'	'	'	'	'	'	'	714,662	568,443	528,723
Europe [Member]	'	'	'	'	'	'	'	'	'	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Revenue	'	'	'	'	'	'	'	'	354,682	291,404	277,971
Asia-Pacific [Member]	'	'	'	'	'	'	'	'	'	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Revenue	'	'	'	'	'	'	'	'	276,442	232,498	197,005
Other markets [Member]	'	'	'	'	'	'	'	'	'	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Revenue	'	'	'	'	'	'	'	'	$75,392	$56,171	$51,836

Segment_Information_Geographic3

Segment Information, Geographic Data, and Significant Customers (Details 1) (USD $)	Dec. 29, 2013	Dec. 30, 2012
In Thousands, unless otherwise specified
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'
Long-Lived Assets	$202,666	$166,167
United States [Member]	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'
Long-Lived Assets	150,470	126,749
United Kingdom [Member]	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'
Long-Lived Assets	24,122	21,740
Singapore [Member]	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'
Long-Lived Assets	21,311	12,504
Other countries [Member]	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'
Long-Lived Assets	$6,763	$5,174

Segment_Information_Geographic4

Segment Information, Geographic Data, and Significant Customers (Details Textual)	0 Months Ended	12 Months Ended
	Dec. 31, 2013	Dec. 29, 2013	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
	segments	segments	Products and Services, Consumables [Member]	Products and Services, Consumables [Member]	Products and Services, Consumables [Member]	Products and Services, Instruments [Member]	Products and Services, Instruments [Member]	Products and Services, Instruments [Member]
Revenue from External Customer [Line Items]	'	'	'	'	'	'	'	'
Number of operating segments	1	2	'	'	'	'	'	'
Number of reportable segments	'	1	'	'	'	'	'	'
Number of future reportable segments	1	'	'	'	'	'	'	'
Percent of sales	'	'	62.00%	64.00%	56.00%	26.00%	27.00%	35.00%

Quarterly_Financial_Informatio2

Quarterly Financial Information (unaudited) (Details) (USD $)	3 Months Ended								12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 29, 2013	Sep. 29, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 30, 2012	Sep. 30, 2012	Jul. 01, 2012	Apr. 01, 2012	Dec. 29, 2013	Dec. 30, 2012	Jan. 01, 2012
Quarterly Financial Information Disclosure [Abstract]	'	'	'	'	'	'	'	'	'	'	'
Fiscal year quarterly operating cycle	'P13W	'P13W	'P13W	'P13W	'P13W	'P13W	'P13W	'P13W	'	'	'
Total revenue	$387,326	$356,800	$346,094	$330,958	$309,265	$285,874	$280,607	$272,770	$1,421,178	$1,148,516	$1,055,535
Gross profit	259,246	209,940	223,409	219,292	203,647	195,873	192,997	181,011	911,887	773,528	709,098
Net (loss) income	$80,661	$31,357	$35,877	($22,587)	$71,903	$29,748	$23,401	$26,202	$125,308	$151,254	$86,628
Net (loss) income per share, basic	$0.64	$0.25	$0.29	($0.18)	$0.58	$0.24	$0.19	$0.21	$1	$1.23	$0.70
Net (loss) income per share, diluted	$0.56	$0.22	$0.26	($0.18)	$0.53	$0.22	$0.18	$0.20	$0.90	$1.13	$0.62

Unsolicited_Tender_Offer_Unsol

Unsolicited Tender Offer Unsolicited Tender Offer (Details Textual) (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 29, 2013	Dec. 30, 2012	Mar. 28, 2012	Jan. 27, 2012
Unsolicited Tender Offer [Abstract]	'	'	'	'
Tender Offer Price Per Share	'	'	'	$44.50
Revised Tender Offer Price Per Share	'	'	$51	'
Unsolicited tender offer related expense	$13,621	$23,136	'	'

SCHEDULE_II_VALUATION_AND_QUAL1

SCHEDULE II - VALUATION AND QUALIFYING ACCOUNTS AND RESERVES (Details) (Allowance for doubtful accounts [Member], USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 29, 2013		Dec. 30, 2012		Jan. 01, 2012
Allowance for doubtful accounts [Member]	'		'		'
Valuation and Qualifying Accounts Disclosure [Line Items]	'		'		'
Balance at Beginning of Period	$4,280		$3,997		$1,686
Additions Charged to (Reductions from) Expense/ Revenue(1)	-422	[1]	2,191	[1]	4,201	[1]
Deductions	-178	[2]	-1,908	[2]	-1,890	[2]
Balance at End of Period	$3,680		$4,280		$3,997
[1]	Additions to and reductions from allowance for doubtful accounts are recorded to selling, general and administrative expense.
[2]	Deductions for allowance for doubtful accounts are for accounts receivable written off.