CONSOLIDATED STATEMENTS OF OPERATIONS - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Commercial revenue:
SPINRAZA royalties	$ 112,540	$ 883	$ 0
Licensing and other royalty revenue	9,519	19,839	2,343
Total commercial revenue	122,059	20,722	2,343
Research and development revenue under collaborative agreements	385,607	325,898	281,360
Total revenue	507,666	346,620	283,703
Expenses:
Research, development and patent	374,644	344,320	322,292
Selling, general and administrative	108,488	48,616	37,173
Total operating expenses	483,132	392,936	359,465
Income (loss) from operations	24,534	(46,316)	(75,762)
Other income (expense):
Investment income	7,805	5,472	4,377
Interest expense	(44,752)	(38,795)	(36,732)
Gain on investment in Regulus Therapeutics Inc.	374	0	20,211
Loss on extinguishment of financing liability for leased facility	(7,689)	0	0
Loss on early retirement of debt	0	(3,983)	0
Other expenses	(3,548)	0	0
Loss before income tax benefit (expense)	(23,276)	(83,622)	(87,906)
Income tax benefit (expense)	5,980	(2,934)	(372)
Net loss	(17,296)	(86,556)	(88,278)
Net loss attributable to noncontrolling interest in Akcea Therapeutics, Inc.	11,326	0	0
Net loss attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ (5,970)	$ (86,556)	$ (88,278)
Basic net income (loss) per share (in dollars per share)	$ 0.08	$ (0.72)	$ (0.74)
Shares used in computing basic net income (loss) per share (in shares)	124,016	120,933	119,719
Diluted net income (loss) per share (in dollars per share)	$ 0.08	$ (0.72)	$ (0.74)
Shares used in computing diluted net income (loss) per share (in shares)	126,098	120,933	119,719