IONIS PHARMACEUTICALS INC — Director's Dealing 2014

Jan 17, 2014

SEC Form 4 — Statement of Changes in Beneficial Ownership

Issuer: ISIS PHARMACEUTICALS INC (ISIS)
CIK: 0000874015
Period of Report: 2014-01-15

Reporting Person: CROOKE STANLEY T (Director, Chairman and CEO)

Non-Derivative Transactions

Date	Security	Code	Shares	Price	A/D	Holdings After	Ownership
2014-01-15	Common Stock	M	5548	—	Acquired	7209	Direct
2014-01-16	Common Stock	S	2112	$47.0812	Disposed	5097	Direct
2014-01-15	Common Stock	M	2978	—	Acquired	8075	Direct
2014-01-16	Common Stock	S	1134	$47.0811	Disposed	6941	Direct
2014-01-15	Common Stock	M	417	—	Acquired	591	Indirect
2014-01-16	Common Stock	S	160	$47.0799	Disposed	431	Indirect
2014-01-15	Common Stock	M	317	—	Acquired	748	Indirect
2014-01-16	Common Stock	S	121	$47.0807	Disposed	627	Indirect

Derivative Transactions

Date	Security	Exercise Price	Code	Shares	A/D	Expiration	Underlying	Ownership
2014-01-15	Restricted Stock Units	$	A	31250	Acquired		Common Stock (31250)	Direct
2014-01-15	Restricted Stock Units	$	A	1416	Acquired		Common Stock (1416)	Indirect
2014-01-15	Restricted Stock Units	$	M	5548	Disposed		Common Stock (5548)	Direct
2014-01-15	Restricted Stock Units	$	M	2978	Disposed		Common Stock (2978)	Direct
2014-01-15	Restricted Stock Units	$	M	417	Disposed		Common Stock (417)	Indirect
2014-01-15	Restricted StockUnits	$	M	317	Disposed		Common Stock (317)	Indirect

Holdings (Non-Derivative)

Security	Shares	Ownership
Common Stock	725391	Indirect

Footnotes

F1: Acquired pursuant to vesting and release of shares pursuant to an RSU award granted on January 30, 2013.

F2: The sale was made pursuant to an automatic sale to cover the required tax withholding obligations pursuant to the 2011 Equity Incentive Plan Restricted Stock Unit Agreement and Grant Notice, dated January 30, 2013.

F3: Acquired pursuant to vesting and release of shares pursuant to an RSU award granted on January 15, 2012.

F4: The sale was made pursuant to an automatic sale to cover the required tax withholding obligations pursuant to the 2011 Equity Incentive Plan Restricted Stock Unit Agreement and Grant Notice, dated January 15, 2012.

F5: Acquired pursuant to vesting and release of shares pursuant to an RSU award granted on January 15, 2013.

F6: The sale was made pursuant to an automatic sale to cover the required tax withholding obligations pursuant to the 2011 Equity Incentive Plan Restricted Stock Unit Agreement and Grant Notice, dated January 15, 2013.

F7: Each Restricted Stock Unit represents a contingent right to receive one share of Isis common stock, or its equivalent cash value.

F8: Grant 1/15/2014 to reporting person of Restricted Stock Units under the Isis Pharmaceuticals, Inc. 2011 Equity Incentive Plan. Restricted Stock Units vest in four equal annual installments, the first installment vesting on January 15, 2015. Upon vesting, the restricted stock units will be paid out in whole shares of Isis common stock or cash as may be determined by the Company. The RSU shall be fully vested on January 15, 2018. The RSU is vested as to 0 shares on January 15, 2014.

F9: Restricted Stock Unit Award granted on January 30, 2013. Restricted Stock Units vest in equal annual installments, the first installment vested on January 15, 2014. Upon vesting, the restricted stock units will be paid out in whole shares of Isis common stock or cash as may be determined by the Company. The RSU shall be fully vested on January 15, 2017.

F10: Restricted Stock Unit Award granted on January 15, 2012. Restricted Stock Units vest in equal annual installments, the first installment vested on January 15, 2013. Upon vesting, the restricted stock units will be paid out in whole shares of Isis common stock or cash as may be determined by the Company. The RSU shall be fully vested on January 15, 2016.

F11: Restricted Stock Unit Award granted on January 15, 2013. Restricted Stock Units vest in equal annual installments, the first installment vested on January 15, 2014. Upon vesting, the restricted stock units will be paid out in whole shares of Isis common stock or cash as may be determined by the Company. The RSU shall be fully vested on January 15, 2017.