Marketable Securities (Details 2) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2011		Sep. 30, 2011
Marketable Securities
Cash equivalents (Alios)	$ 51,878	[1]	$ 0

[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.