Condensed Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Jun. 30, 2013		Jun. 30, 2012
Cash flows from operating activities:
Net income (loss)	$ (374,339)		$ 53,408
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation and amortization expense	21,245		17,225
Stock-based compensation expense	72,625		59,067
Other non-cash based compensation expense	5,857		5,469
Intangible asset impairment charge	412,900		0
Deferred income taxes	(130,661)		19,310
Write-down of inventories to net realizable value	5,083		78,000
Other non-cash items, net	755		130
Changes in operating assets and liabilities:
Accounts receivable, net	(18,462)		(2,483)
Inventories	(6,620)		34,288
Prepaid expenses and other current assets	(18,152)		(40,053)
Accounts payable	(53,374)		(15,313)
Accrued expenses and other liabilities	11,316		9,310
Excess tax benefit from share-based payment arrangements	0		1,214
Accrued restructuring expense	(1,276)		(1,483)
Deferred revenues	(6,842)		(25,764)
Net cash provided by (used in) operating activities	(66,705)		121,321
Cash flows from investing activities:
Purchases of marketable securities	(898,706)		(777,604)
Sales and maturities of marketable securities	830,906		502,188
Expenditures for property and equipment	(18,408)		(21,698)
Decrease (increase) in restricted cash	31,812		0
Decrease (increase) in restricted cash and cash equivalents (Alios)	11,695		(4,146)
Decrease (increase) in other assets	(414)		485
Net cash used in investing activities	(42,287)		(301,745)
Cash flows from financing activities:
Excess tax benefit from share-based payment arrangements	0		1,214
Issuances of common stock from employee benefit plans	207,872		158,003
Payments to redeem secured notes (due 2015)	(158)		0
Payments on capital lease obligations	(12,246)		0
Payments on construction financing lease obligation	(44,115)		0
Net cash provided by (used in) financing activities	151,353		159,217
Effect of changes in exchange rates on cash	(521)		(52)
Net increase (decrease) in cash and cash equivalents	41,840		(21,259)
Cash and cash equivalents—beginning of period	489,407	[1]	475,320
Cash and cash equivalents—end of period	531,247	[1]
Supplemental disclosure of cash flow information:
Cash paid for interest	6,700		6,700
Conversion of convertible senior subordinated notes (due 2015) for common stock	399,842		0
Interest on converted convertible senior subordinated notes (due 2015) offset to additional paid-in capital	6,700		0
Unamortized debt issuance costs of converted convertible subordinated notes (due 2015) offset to additional paid-in capital	4,230		0
Capitalization of construction in-process related to construction financing lease obligation	130,222		104,341
Assets acquired under capital lease	$ 21,576		$ 29,072

[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 C, "Collaborative Arrangements," to these condensed consolidated financial statements for amounts.