Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012		Dec. 31, 2011		Dec. 31, 2010
Cash flows from operating activities:
Net income (loss)	$ (51,135)		$ 41,179		$ (754,626)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation and amortization expense	38,191		35,041		30,459
Stock-based compensation expense	114,285		118,226		91,124
Other non-cash based compensation expense	10,261		8,525		6,552
Intangible asset impairment charge	0		105,800		0
Secured notes (due 2012) discount amortization expense	0		18,409		13,589
Change in fair value of derivative instruments	0		16,801		41,229
Deferred income taxes	36,660		(7,501)		0
Loss on disposal of property and equipment	390		55		39
Write-downs of inventories to net realizable value	133,189		0		0
Other non-cash items, net	(212)		264		(31)
Changes in operating assets and liabilities, excluding the effects of the acquisition of a variable interest entity (Alios):
Accounts receivable, net	39,912		(170,606)		(2,923)
Inventories	(29,925)		(111,388)		0
Prepaid expenses and other current assets	(12,259)		(1,717)		(600)
Accounts payable	14,892		37,468		(1,182)
Accrued expenses and other liabilities	29,232		116,822		11,213
Excess tax benefit from share-based payment arrangements	(1,971)		(900)		0
Accrued restructuring expense	(2,985)		(3,282)		(4,422)
Income taxes payable (Alios)	(11,360)		12,075		0
Deferred revenues	(39,324)		(71,536)		(65,863)
Net cash provided by (used in) operating activities	267,841		143,735		(635,442)
Cash flows from investing activities:
Purchases of marketable securities	(1,705,829)		(721,545)		(1,234,719)
Sales and maturities of marketable securities	1,367,927		1,016,040		1,284,806
Payment for acquisition of a variable interest entity (Alios)	0		(60,000)		0
Expenditures for property and equipment	(71,140)		(34,595)		(38,054)
Decrease (increase) in restricted cash and cash equivalents	2,156		0		(3,777)
Decrease (increase) in restricted cash and cash equivalents (Alios)	(18,105)		12,695		0
Decrease (increase) in other assets	(826)		(183)		(955)
Net cash provided by (used in) investing activities	(425,817)		212,412		7,301
Cash flows from financing activities:
Excess tax benefit from share-based payment arrangements	1,971		900		0
Issuances of common stock from employee benefit plans	191,721		124,862		33,434
Issuance of convertible senior subordinated notes (due 2015)	0		0		391,645
Payments to redeem secured notes (due 2012)	0		(155,000)		0
Settlement of milestone derivatives	0		(95,000)		0
Payments on capital lease obligations	(2,615)		0		0
Payments on construction financing lease obligation	(18,873)		0		0
Debt conversion costs	0		0		(22)
Net cash provided by (used in) financing activities	172,204		(124,238)		425,057
Effect of changes in exchange rates on cash	(141)		214		(377)
Net increase (decrease) in cash and cash equivalents	14,087		232,123		(203,461)
Cash and cash equivalents—beginning of period	475,320	[1]	243,197		446,658
Cash and cash equivalents—end of period	489,407	[1]	475,320	[1]	243,197
Supplemental disclosure of cash flow information:
Cash paid for interest	13,400		13,512		761
Cash paid for income taxes	9,318		0		0
Conversion of convertible senior subordinated notes (due 2013) for common stock	0		0		32,071
Accrued interest offset to additional paid-in capital on conversion of convertible senior subordinated notes (due 2013)	0		0		140
Unamortized debt issuance costs of converted convertible senior subordinated notes (due 2013) offset to additional paid-in capital	0		0		624
Capitalization of construction in-process related to construction financing lease obligation	235,594		54,655		0
Assets acquired under capital lease obligations	$ 30,101		$ 0		$ 0

[1] Amounts include the assets and liabilities of Vertex’s variable interest entity (“VIE”), Alios BioPharma, Inc. (“Alios”). Vertex’s interests and obligations with respect to the VIE’s assets and liabilities are limited to those accorded to Vertex in its agreement with Alios. See Note B, "Collaborative Arrangements," to these consolidated financial statements for amounts.