CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2009
Operating activities:
Net income (loss)	$ (84,801)	$ (61,251)	$ 150,672
Adjustments to reconcile net income (loss) to net cash used in operating activities:
Depreciation	6,594	4,840	3,935
Amortization of patents	1,938	1,961	3,024
Amortization of licenses	3,252	2,376	2,344
Amortization of premium on investments, net	5,410	5,075	2,026
Amortization of debt issuance costs	507	507	507
Amortization of 2 5/8 percent convertible subordinated notes discount	8,553	7,795	7,107
Share-based compensation expense	9,845	12,159	13,385
Equity in net loss of Regulus Therapeutics Inc.	3,554	2,228
Gain from sale of Ibis Biosciences, Inc. to Abbott Molecular Inc.			(185,657)
Gain from the sale of property, plant and equipment		(72)
(Gain) loss on investments, net	(4,182)	713	(2,084)
Non-cash losses related to patents, licensing and property, plant and equipment	1,924	1,512	696
Excess tax benefits on share-based compensation			(278)
Changes in operating assets and liabilities:
Contracts receivable	(5,679)	10,479	(6,778)
Inventories	(1,655)	284	(17)
Other current and long-term assets	914	(943)	(955)
Accounts payable	875	1,325	(3,652)
Accrued compensation	2,352	394	(4,371)
Income taxes payable		(7,178)	(10,013)
Deferred rent	382
Accrued liabilities	6,273	1,013	4,318
Deferred contract revenue	(70,857)	(46,810)	(82,650)
Net cash used in operating activities	(114,801)	(63,593)	(108,441)
Investing activities:
Purchases of short-term investments	(371,108)	(530,137)	(776,381)
Proceeds from the sale of short-term investments	488,918	577,533	578,886
Purchases of property, plant and equipment	(7,331)	(13,237)	(13,414)
Proceeds from the sale of property, plant and equipment		185
Proceeds from land sold to BioMed		10,147
Reduction of cash due to deconsolidation of Regulus Therapeutics Inc. upon adoption of a new accounting standard		(16,228)
Acquisition of licenses and other assets, net	(3,667)	(4,319)	(2,880)
Purchases of strategic investments, net of proceeds received	(359)	(250)	(1,349)
Proceeds from the sale of strategic investments	4,445		2,848
Net cash provided by (used in) investing activities	110,898	23,694	(212,290)
Financing activities:
Proceeds from issuance of equity	3,567	4,356	13,156
Excess tax benefits on share-based compensation			278
Proceeds from equipment financing arrangement	1,625	4,694	6,394
Principal payments on debt and capital lease obligations	(5,864)	(4,354)	(2,827)
Proceeds from sale of Ibis Biosciences, Inc to Abbott Molecular Inc.			175,000
Proceeds from Alnylam's capital contribution to Regulus Therapeutics Inc.			10,000
Net cash (used in) provided by financing activities	(672)	4,696	202,001
Net decrease in cash and cash equivalents	(4,575)	(35,203)	(118,730)
Cash and cash equivalents at beginning of year	70,052	105,255	223,985
Cash and cash equivalents at end of year	65,477	70,052	105,255
Supplemental disclosures of cash flow information:
Interest paid	4,804	4,889	4,883
Income taxes paid, net of refund received	2	7,270	13,205
Supplemental disclosures of non-cash investing and financing activities:
Amounts accrued for capital and patent expenditures	902	922	870
Capital lease obligations		770
Capitalized costs and financing liability associated with leased facility	$ 59,730