Condensed Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Mar. 31, 2013		Dec. 31, 2012
Current assets:
Cash and cash equivalents	$ 379,099	[1]	$ 489,407	[1]
Marketable securities, available for sale	860,255	[1]	831,808	[1]
Restricted cash and cash equivalents (Alios)	63,008	[1]	69,983	[1]
Accounts receivable, net	194,054	[1]	143,250	[1]
Inventories	21,532	[1]	30,464	[1]
Prepaid expenses and other current assets	47,835	[1]	24,673	[1]
Total current assets	1,565,783	[1]	1,589,585	[1]
Restricted cash	31,934	[1]	31,934	[1]
Property and equipment, net	504,232	[1]	433,609	[1]
Intangible assets	250,600	[1]	663,500	[1]
Goodwill	30,992	[1]	30,992	[1]
Other assets	8,693	[1]	9,668	[1]
Total assets	2,392,234	[1]	2,759,288	[1]
Current liabilities:
Accounts payable	59,627	[1]	101,292	[1]
Accrued expenses	274,061	[1]	264,884	[1]
Deferred revenues, current portion	35,533	[1]	27,566	[1]
Accrued restructuring expense, current portion	4,911	[1]	4,758	[1]
Capital lease obligations, current portion	8,302	[1]	13,707	[1]
Other liabilities, current portion	25,205	[1]	20,417	[1]
Total current liabilities	407,639	[1]	432,624	[1]
Deferred revenues, excluding current portion	90,297	[1]	96,242	[1]
Accrued restructuring expense, excluding current portion	17,548	[1]	18,570	[1]
Capital lease obligations, excluding current portion	14,755	[1]	15,170	[1]
Convertible senior subordinated notes (due 2015)	400,000	[1]	400,000	[1]
Deferred tax liability	151,664	[1]	280,367	[1]
Construction financing lease obligation	316,821	[1]	268,031	[1]
Other liabilities, excluding current portion	16,678	[1]	13,902	[1]
Total liabilities	1,415,402	[1]	1,524,906	[1]
Commitments and contingencies		[1]		[1]
Redeemable noncontrolling interest (Alios)	38,872	[1]	38,530	[1]
Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding at March 31, 2013 and December 31, 2012	0	[1]	0	[1]
Common stock, $0.01 par value; 300,000,000 shares authorized at March 31, 2013 and December 31, 2012; 218,651,704 and 217,286,868 shares issued and outstanding at March 31, 2013 and December 31, 2012, respectively	2,160	[1]	2,149	[1]
Additional paid-in capital	4,574,987	[1]	4,519,448	[1]
Accumulated other comprehensive loss	(1,149)	[1]	(550)	[1]
Accumulated deficit	(3,829,883)	[1]	(3,521,867)	[1]
Total Vertex shareholders’ equity	746,115	[1]	999,180	[1]
Noncontrolling interest (Alios)	191,845	[1]	196,672	[1]
Total shareholders’ equity	937,960	[1]	1,195,852	[1]
Total liabilities and shareholders’ equity	$ 2,392,234	[1]	$ 2,759,288	[1]

[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.