Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012		Dec. 31, 2011
Current assets:
Cash and cash equivalents	$ 489,407	[1]	$ 475,320	[1]
Marketable securities, available for sale	831,808	[1]	493,602	[1]
Restricted cash and cash equivalents (Alios)	69,983	[1]	51,878	[1]
Accounts receivable, net	143,250	[1]	183,135	[1]
Inventories	30,464	[1]	112,430	[1]
Prepaid expenses and other current assets	24,673	[1]	14,889	[1]
Total current assets	1,589,585	[1]	1,331,254	[1]
Restricted cash	31,934	[1]	34,090	[1]
Property and equipment, net	433,609	[1]	133,176	[1]
Intangible assets	663,500	[1]	663,500	[1]
Goodwill	30,992	[1]	30,992	[1]
Other assets	9,668	[1]	11,268	[1]
Total assets	2,759,288	[1]	2,204,280	[1]
Current liabilities:
Accounts payable	101,292	[1]	74,642	[1]
Accrued expenses	264,884	[1]	243,187	[1]
Deferred revenues, current portion	27,566	[1]	45,037	[1]
Accrued restructuring expense, current portion	4,758	[1]	4,932	[1]
Capital lease obligations, current portion	13,707		0
Income taxes payable (Alios)	715	[1]	12,075	[1]
Other liabilities, current portion	19,702	[1]	12,475	[1]
Total current liabilities	432,624	[1]	392,348	[1]
Deferred revenues, excluding current portion	96,242	[1]	118,095	[1]
Accrued restructuring expense, excluding current portion	18,570	[1]	21,381	[1]
Capital lease obligations, excluding current portion	15,170		0
Convertible senior subordinated notes (due 2015)	400,000	[1]	400,000	[1]
Deferred tax liability	280,367	[1]	243,707	[1]
Construction financing lease obligation	268,031	[1]	55,950	[1]
Other liabilities, excluding current portion	13,902	[1]	7,287	[1]
Total liabilities	1,524,906	[1]	1,238,768	[1]
Commitments and contingencies (Note S and Note U)		[1]		[1]
Redeemable noncontrolling interest (Alios)	38,530	[1]	37,036	[1]
Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding at December 31, 2012 and 2011	0	[1]	0	[1]
Common stock, $0.01 par value; 300,000,000 shares authorized at December 31, 2012 and 2011; 217,286,868 and 209,303,995 shares issued and outstanding at December 31, 2012 and 2011, respectively	2,149	[1]	2,072	[1]
Additional paid-in capital	4,519,448	[1]	4,200,659	[1]
Accumulated other comprehensive loss	(550)	[1]	(1,053)	[1]
Accumulated deficit	(3,521,867)	[1]	(3,414,835)	[1]
Total Vertex shareholders’ equity	999,180	[1]	786,843	[1]
Noncontrolling interest (Alios)	196,672	[1]	141,633	[1]
Total shareholders’ equity	1,195,852	[1]	928,476	[1]
Total liabilities and shareholders’ equity	$ 2,759,288	[1]	$ 2,204,280	[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 B, "Collaborative Arrangements," to these consolidated financial statements for amounts.