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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 |

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