CONSOLIDATED STATEMENTS OF OPERATIONS (USD $) In Thousands, except Per Share data, unless otherwise specified	12 Months Ended
	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2009
Revenue:
Research and development revenue under collaborative agreements	$ 96,190	$ 102,921	$ 108,131
Licensing and royalty revenue	2,896	5,552	13,469
Total revenue	99,086	108,473	121,600
Expenses:
Research and development	157,397	145,160	134,623
General and administrative	12,789	11,669	14,515
Total operating expenses	170,186	156,829	149,138
Loss from operations	(71,100)	(48,356)	(27,538)
Other income (expense):
Equity in net loss of Regulus Therapeutics Inc.	(3,554)	(2,228)
Investment income	2,414	3,370	6,361
Interest expense	(16,732)	(13,232)	(12,672)
Gain (loss) on investments, net	4,182	(713)	2,084
Loss from continuing operations, before income tax expense	(84,790)	(61,159)	(31,765)
Income tax expense	(11)	(92)	(3,191)
Net loss from continuing operations	(84,801)	(61,251)	(34,956)
Discontinued operations:
Loss from discontinued operations			(29)
Gain on sale of Ibis Biosciences, Inc., net of tax			185,657
Net income from discontinued operations, net of tax			185,628
Net income (loss)	(84,801)	(61,251)	150,672
Net loss attributable to noncontrolling interest in Regulus Therapeutics Inc.			4,394
Net income (loss) attributable to Isis Pharmaceuticals, Inc. common stockholders	$ (84,801)	$ (61,251)	$ 155,066
Basic and diluted net income (loss) per share:
Net loss from continuing operations attributable to Isis Pharmaceuticals, Inc. common stockholders, Basic (in dollars per share)	$ (0.85)	$ (0.62)	$ (0.31)
Net income from discontinued operations, Basic (in dollars per share)			$ 1.89
Basic net income (loss) attributable to Isis Pharmaceuticals, Inc. common stockholders (in dollars per share)	$ (0.85)	$ (0.62)	$ 1.58
Net loss from continuing operations attributable to Isis Pharmaceuticals, Inc. common stockholders, Diluted (in dollars per share)	$ (0.85)	$ (0.62)	$ (0.31)
Net income from discontinued operations, Diluted (in dollars per share)			$ 1.89
Diluted net income (loss) attributable to Isis Pharmaceuticals, Inc. common stockholders (in dollars per share)	$ (0.85)	$ (0.62)	$ 1.58
Shares used in computing basic net income (loss) per share (in shares)	99,656	99,143	98,109
Shares used in computing diluted net income (loss) per share (in shares)	99,656	99,143	98,109