Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2013		Dec. 31, 2012		Dec. 31, 2011
Cash flows from operating activities:
Net income (loss)	$ (687,550)		$ (51,135)		$ 41,179
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation and amortization expense	48,365		38,191		35,041
Stock-based compensation expense	127,303		114,285		118,226
Other non-cash based compensation expense	5,860		10,261		8,525
Intangible asset impairment charges	663,500		0		105,800
Secured notes (due 2012) discount amortization expense	0		0		18,409
Change in fair value of free-standing derivatives related to the sale of milestone payments	0		0		16,801
Deferred income taxes	(285,053)		36,660		(7,501)
Non-cash Expense	7,594		0		0
Deconsolidation of variable interest entity (Alios)	55,110		0		0
Write-downs of inventories to net realizable value	10,358		133,189		0
Excess tax benefit from share-based payment arrangements	1,252		(1,971)		(900)
Other non-cash items, net	6,742		178		319
Changes in operating assets and liabilities, excluding the effects of the acquisition and deconsolidation of a variable interest entity (Alios):
Accounts receivable, net	53,363		39,912		(170,606)
Inventories	7,142		(29,925)		(111,388)
Prepaid expenses and other current assets	(12,061)		(23,619)		10,358
Accounts payable	(49,234)		14,892		37,468
Accrued expenses and other liabilities	43,725		29,232		116,822
Accrued restructuring expense	5,025		(2,985)		(3,282)
Deferred revenues	(53,011)		(39,324)		(71,536)
Net cash provided by (used in) operating activities	(51,570)		267,841		143,735
Cash flows from investing activities:
Purchases of marketable securities	(2,412,418)		(1,705,829)		(721,545)
Sales and maturities of marketable securities	2,348,295		1,367,927		1,016,040
Payment for acquisition of variable interest entity (Alios)	0		0		(60,000)
Expenditures for property and equipment	(51,393)		(71,140)		(34,595)
Decrease in restricted cash and cash equivalents	31,804		2,156		0
Decrease (increase) in restricted cash and cash equivalents (Alios)	27,884		(18,105)		12,695
Decrease (increase) in other assets	1,698		(826)		(183)
Net cash provided by (used in) investing activities	(54,130)		(425,817)		212,412
Cash flows from financing activities:
Excess tax benefit from share-based payment arrangements	(1,252)		1,971		900
Issuances of common stock under benefit plans	265,878		191,721		124,862
Payments to redeem secured notes	(158)		0		(155,000)
Settlement of milestone derivatives	0		0		(95,000)
Payments on capital lease obligations	(16,057)		(2,615)		0
Payments on construction financing lease obligation	(67,527)		(18,873)		0
Net cash provided by (used in) financing activities	180,884		172,204		(124,238)
Effect of changes in exchange rates on cash	4,708		(141)		214
Net increase in cash and cash equivalents	79,892		14,087		232,123
Cash and cash equivalents—beginning of period	489,407	[1]	475,320		243,197
Cash and cash equivalents—end of period	569,299	[1]	489,407	[1]	475,320
Supplemental disclosure of cash flow information:
Cash paid for interest	11,015		13,400		13,512
Cash paid for income taxes	2,840		9,318		0
Conversion of convertible senior subordinated notes (due 2015) for common stock	399,842		0		0
Capitalization of construction in-process related to construction financing lease obligation	215,013		235,594		54,655
Assets acquired under capital lease obligations	50,972		30,101		0
Unamortized deferred debt issuance costs exchanged	$ 4,230		$ 0		$ 0

[1] Amounts as of December 31, 2012 include the assets and liabilities of Vertex’s variable interest entity (“VIE”), Alios BioPharma, Inc. (“Alios”). The Company deconsolidated Alios as of December 31, 2013. 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.