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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 |
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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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