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Organization and Significant Accounting Policies, Revenue Recognition - Adoption of Topic 606 (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended								12 Months Ended
	May 31, 2015	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Consolidated Balance Sheet [Abstract]
Current portion of deferred contract revenue		$ 160,256				$ 125,336				$ 160,256	$ 125,336
Long-term deferred contract revenue		567,359				108,026				567,359	108,026
Accumulated deficit		(967,293)				(1,241,034)				(967,293)	(1,241,034)
Noncontrolling interest in Akcea Therapeutics, Inc.		139,081				84,267				139,081	84,267
Total stockholders' equity		1,187,160				365,280				1,187,160	365,280	$ 39,613	$ 200,790
Consolidated Statements of Operations [Abstract]
Revenue	$ 91,200									599,674	514,179	372,776
Income (loss) from operations		10,782	$ (18,572)	$ (50,281)	$ (3,301)	(6,200)	$ 11,312	$ 6,450	$ 19,485	(61,372)	31,047	(20,160)
Net income (loss)		302,735	(20,365)	(56,573)	(10,812)	(9,169)	(7,493)	(3,085)	8,964	214,985	(10,783)	(60,400)
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders		320,078	(4,559)	(40,358)	(1,420)	(2,922)	(2,611)	(3,085)	8,964	273,741	$ 346	$ (60,400)
Net income (loss) per share, basic and diluted (in dollars per share)											$ 0.15	$ (0.50)
Consolidated Statements of Cash Flows [Abstract]
Net income (loss)		302,735	$ (20,365)	$ (56,573)	(10,812)	(9,169)	$ (7,493)	$ (3,085)	8,964	214,985	$ (10,783)	$ (60,400)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities [Abstract]
Deferred contract revenue										494,254	30,182	(85,306)
Cash and cash equivalents at beginning of year					129,630				84,685	129,630	84,685	128,797
Cash and cash equivalents at end of year		$ 278,820				129,630				278,820	129,630	84,685
Commercial Revenue [Member]
Consolidated Statements of Operations [Abstract]
Revenue										254,922	120,014	22,767
SPINRAZA Royalties [Member]
Consolidated Statements of Operations [Abstract]
Revenue										237,930	112,540	883
Licensing and Other Royalty Revenue [Member]
Consolidated Statements of Operations [Abstract]
Revenue										14,755	7,474	21,884
Research and Development Revenue Under Collaborative Agreements [Member]
Consolidated Statements of Operations [Abstract]
Revenue										344,752	394,165	350,009
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities [Abstract]
Increase in revenue from amortization of milestone payments achieved under new revenue guidance											23,700	24,100
Decrease in revenue from amortization of payments using input method under new revenue guidance											(15,100)	0
Topic 606 [Member]
Revenue Recognition [Abstract]
Cumulative effect of adoption on retained earnings						(86,100)					(86,100)
Topic 606 [Member] | As Previously Reported Under Topic 605 [Member]
Consolidated Balance Sheet [Abstract]
Current portion of deferred contract revenue						106,465					106,465
Long-term deferred contract revenue						72,708					72,708
Accumulated deficit						(1,187,398)					(1,187,398)
Noncontrolling interest in Akcea Therapeutics, Inc.						87,847					87,847
Total stockholders' equity						418,719					418,719
Consolidated Statements of Operations [Abstract]
Revenue											507,666	346,620
Income (loss) from operations											24,534	(46,316)
Net income (loss)											(17,296)	(86,556)
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders											$ (5,970)	$ (86,556)
Net income (loss) per share, basic and diluted (in dollars per share)											$ 0.08	$ (0.72)
Consolidated Statements of Cash Flows [Abstract]
Net income (loss)											$ (17,296)	$ (86,556)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities [Abstract]
Deferred contract revenue											36,695	(59,150)
Cash and cash equivalents at beginning of year					129,630				84,685	129,630	84,685	128,797
Cash and cash equivalents at end of year						129,630					129,630	84,685
Topic 606 [Member] | As Previously Reported Under Topic 605 [Member] | Commercial Revenue [Member]
Consolidated Statements of Operations [Abstract]
Revenue											122,059	20,722
Topic 606 [Member] | As Previously Reported Under Topic 605 [Member] | SPINRAZA Royalties [Member]
Consolidated Statements of Operations [Abstract]
Revenue											112,540	883
Topic 606 [Member] | As Previously Reported Under Topic 605 [Member] | Licensing and Other Royalty Revenue [Member]
Consolidated Statements of Operations [Abstract]
Revenue											9,519	19,839
Topic 606 [Member] | As Previously Reported Under Topic 605 [Member] | Research and Development Revenue Under Collaborative Agreements [Member]
Consolidated Statements of Operations [Abstract]
Revenue											385,607	325,898
Topic 606 [Member] | Topic 606 Adjustment [Member]
Consolidated Balance Sheet [Abstract]
Current portion of deferred contract revenue						18,871					18,871
Long-term deferred contract revenue						35,318					35,318
Accumulated deficit						(53,636)					(53,636)
Noncontrolling interest in Akcea Therapeutics, Inc.						(3,580)					(3,580)
Total stockholders' equity						(53,439)					(53,439)
Consolidated Statements of Operations [Abstract]
Revenue											6,513	26,156
Income (loss) from operations											6,513	26,156
Net income (loss)											6,513	26,156
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders											$ 6,316	$ 26,156
Net income (loss) per share, basic and diluted (in dollars per share)											$ 0.07	$ 0.22
Consolidated Statements of Cash Flows [Abstract]
Net income (loss)											$ 6,513	$ 26,156
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities [Abstract]
Deferred contract revenue											(6,513)	(26,156)
Cash and cash equivalents at beginning of year					$ 0				$ 0	$ 0	0	0
Cash and cash equivalents at end of year						$ 0					0	0
Topic 606 [Member] | Topic 606 Adjustment [Member] | Commercial Revenue [Member]
Consolidated Statements of Operations [Abstract]
Revenue											(2,045)	2,045
Topic 606 [Member] | Topic 606 Adjustment [Member] | SPINRAZA Royalties [Member]
Consolidated Statements of Operations [Abstract]
Revenue											0	0
Topic 606 [Member] | Topic 606 Adjustment [Member] | Licensing and Other Royalty Revenue [Member]
Consolidated Statements of Operations [Abstract]
Revenue											(2,045)	2,045
Topic 606 [Member] | Topic 606 Adjustment [Member] | Research and Development Revenue Under Collaborative Agreements [Member]
Consolidated Statements of Operations [Abstract]
Revenue											$ 8,558	$ 24,111

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