Significant Accounting Policies, Revenue Recognition - Adoption of Topic 606 (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended		12 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Dec. 31, 2017
Condensed Consolidated Balance Sheet [Abstract]
Current portion of deferred revenue	$ 157,145		$ 157,145		$ 125,336
Long-term portion of deferred revenue	523,384		523,384		108,026
Accumulated deficit	(1,287,369)		(1,287,369)		(1,241,034)
Noncontrolling interest in Akcea Therapeutics, Inc.	129,594		129,594		84,267
Total stockholders' equity	840,144		840,144		365,280
Condensed Consolidated Statement of Operations [Abstract]
Revenue	145,395	$ 118,314	407,559	$ 346,387
Income (loss) from operations	(18,572)	11,312	(72,157)	37,247
Net income (loss)	(20,365)	(7,493)	(87,747)	(1,616)
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ (4,559)	$ (2,611)	$ (46,335)	$ 3,266
Net income (loss) per share, basic (in dollars per share)	$ (0.03)	$ (0.02)	$ (0.33)	$ 0.13
Net income per share, diluted (in dollars per share)	$ (0.03)	$ (0.02)	$ (0.33)	$ 0.13
Condensed Consolidated Statement of Cash Flows [Abstract]
Net income (loss)	$ (20,365)	$ (7,493)	$ (87,747)	$ (1,616)
Adjustments to reconcile net income (loss) to net cash provided by operating activities [Abstract]
Deferred contract revenue			447,168	31,071
Cash and cash equivalents at beginning of period			129,630	84,685	84,685
Cash and cash equivalents at end of period	479,891	159,184	479,891	159,184	129,630
Increase in revenue from amortization of milestone payments achieved under new revenue guidance		500		27,900
Decrease in revenue from amortization of payments using input method under new revenue guidance		(4,000)		(17,500)
Commercial Revenue [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue	82,756	34,617	181,975	66,106
SPINRAZA Royalties [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue	70,010	32,890	167,743	60,467
Licensing and Other Royalty Revenue [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue	12,746	1,727	14,232	5,639
Research and Development Revenue Under Collaborative Agreements [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue	$ 62,639	83,697	$ 225,584	280,281
Topic 606 [Member]
Revenue Recognition [Abstract]
Cumulative effect of adoption on retained earnings					(53,600)
Topic 606 [Member] | As Previously Reported Under Topic 605 [Member]
Condensed Consolidated Balance Sheet [Abstract]
Current portion of deferred revenue					106,465
Long-term portion of deferred revenue					72,708
Accumulated deficit					(1,187,398)
Noncontrolling interest in Akcea Therapeutics, Inc.					87,847
Total stockholders' equity					418,719
Condensed Consolidated Statement of Operations [Abstract]
Revenue		120,911		335,367
Income (loss) from operations		13,909		26,227
Net income (loss)		(4,896)		(12,636)
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders		$ (976)		$ (8,716)
Net income (loss) per share, basic (in dollars per share)		$ 0		$ 0.02
Net income per share, diluted (in dollars per share)		$ 0		$ 0.02
Condensed Consolidated Statement of Cash Flows [Abstract]
Net income (loss)		$ (4,896)		$ (12,636)
Adjustments to reconcile net income (loss) to net cash provided by operating activities [Abstract]
Deferred contract revenue				42,091
Cash and cash equivalents at beginning of period				84,685	84,685
Cash and cash equivalents at end of period		159,184		159,184
Topic 606 [Member] | As Previously Reported Under Topic 605 [Member] | Commercial Revenue [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue		33,769		65,450
Topic 606 [Member] | As Previously Reported Under Topic 605 [Member] | SPINRAZA Royalties [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue		32,890		60,467
Topic 606 [Member] | As Previously Reported Under Topic 605 [Member] | Licensing and Other Royalty Revenue [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue		879		4,983
Topic 606 [Member] | As Previously Reported Under Topic 605 [Member] | Research and Development Revenue Under Collaborative Agreements [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue		87,142		269,917
Topic 606 [Member] | Topic 606 Adjustment [Member]
Condensed Consolidated Balance Sheet [Abstract]
Current portion of deferred revenue					18,871
Long-term portion of deferred revenue					35,318
Accumulated deficit					(53,636)
Noncontrolling interest in Akcea Therapeutics, Inc.					(3,580)
Total stockholders' equity					(53,439)
Condensed Consolidated Statement of Operations [Abstract]
Revenue		(2,597)		11,020
Income (loss) from operations		(2,597)		11,020
Net income (loss)		(2,597)		11,020
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders		$ (1,635)		$ 11,982
Net income (loss) per share, basic (in dollars per share)		$ (0.02)		$ 0.11
Net income per share, diluted (in dollars per share)		$ (0.02)		$ 0.11
Condensed Consolidated Statement of Cash Flows [Abstract]
Net income (loss)		$ (2,597)		$ 11,020
Adjustments to reconcile net income (loss) to net cash provided by operating activities [Abstract]
Deferred contract revenue				(11,020)
Cash and cash equivalents at beginning of period				0	$ 0
Cash and cash equivalents at end of period		0		0
Topic 606 [Member] | Topic 606 Adjustment [Member] | Commercial Revenue [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue		848		656
Topic 606 [Member] | Topic 606 Adjustment [Member] | SPINRAZA Royalties [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue		0		0
Topic 606 [Member] | Topic 606 Adjustment [Member] | Licensing and Other Royalty Revenue [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue		848		656
Topic 606 [Member] | Topic 606 Adjustment [Member] | Research and Development Revenue Under Collaborative Agreements [Member]
Condensed Consolidated Statement of Operations [Abstract]
Revenue		$ (3,445)		$ 10,364