Accrued Expenses and Other Liabilities, Current Portion (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2013		Dec. 31, 2012
Accrued expenses
Product revenue allowances	$ 85,510		$ 69,936
Payroll and benefits	76,785		62,140
Research, development and commercial contract costs	52,468		63,960
Royalty payable	18,334		29,007
Other	16,241		18,932
Professional fees	10,593		11,226
Taxes payable	8,362		2,182
Unrecognized tax benefits	2,784		4,106
Interest	0		3,395
Total	271,077	[1]	264,884	[1]
Deferred rent	16,652		14,302
Customer deposits	7,692		0
Other	392		5,400
Total	$ 24,736	[1]	$ 19,702	[1]

[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.