IONIS PHARMACEUTICALS INC — Director's Dealing 2012

Sep 6, 2012

SEC Form 4 — Statement of Changes in Beneficial Ownership

Issuer: ISIS PHARMACEUTICALS INC (ISIS)
CIK: 0000874015
Period of Report: 2012-09-04

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

Non-Derivative Transactions

Date	Security	Code	Shares	Price	A/D	Holdings After	Ownership
2012-09-04	Common Stock	M	30000	$5.25	Acquired	30000	Direct
2012-09-04	Common Stock	S	30000	$14.1085	Disposed	0	Direct
2012-09-05	Common Stock	M	15000	$5.25	Acquired	15000	Direct
2012-09-05	Common Stock	S	15000	$14.823	Disposed	0	Direct
2012-09-06	Common Stock	M	8694	$5.25	Acquired	8694	Direct
2012-09-06	Common Stock	S	8694	$15.002	Disposed	0	Direct
2012-09-06	Common Stock	M	8694	$5.25	Acquired	8694	Direct
2012-09-06	Common Stock	S	8694	$15.035	Disposed	0	Direct
2012-09-06	Common Stock	M	1925	$6.84	Acquired	1925	Indirect
2012-09-06	Common Stock	S	1925	$15.035	Disposed	0	Indirect
2012-09-06	Common Stock	M	4381	$5.25	Acquired	4381	Indirect
2012-09-06	Common Stock	S	4381	$15.035	Disposed	0	Indirect
2012-09-06	Common Stock	M	306	$5.25	Acquired	306	Indirect
2012-09-06	Common Stock	S	306	$15.002	Disposed	0	Indirect
2012-09-06	Common Stock	M	6000	$5.25	Acquired	6000	Indirect
2012-09-06	Common Stock	S	6000	$15.002	Disposed	0	Indirect

Derivative Transactions

Date	Security	Exercise Price	Code	Shares	A/D	Expiration	Underlying	Ownership
2012-09-04	Employee Stock Option (right to buy)	$5.25	M	30000	Disposed	2013-01-02	Common Stock (30000)	Direct
2012-09-05	Employee Stock Option (right to buy)	$5.25	M	15000	Disposed	2013-01-02	Common Stock (15000)	Direct
2012-09-06	Employee Stock Option (right to buy)	$5.25	M	17388	Disposed	2013-01-02	Common Stock (17388)	Direct
2012-09-06	Employee Stock Option (right to buy)	$6.84	M	1925	Disposed	2013-01-01	Common Stock (1925)	Indirect
2012-09-06	Employee Stock Option (right to buy)	$5.25	M	4687	Disposed	2013-05-06	Common Stock (4687)	Indirect
2012-09-06	Employee Stock Option (right to buy)	$5.25	M	6000	Disposed	2013-01-02	Common Stock (6000)	Indirect

Holdings (Non-Derivative)

Security	Shares	Ownership
Common Stock	875391	Indirect

Footnotes

F1: Acquired as a result of exercising a stock option pursuant to a Rule 10b5-1 Trading Plan. The purchase and sale reported on this Form 4 was effective pursuant to a Rule 10b5-1 Trading Plan adopted by the reporting person on 6/27/2012.

F2: Acquired as a result of exercising a stock option pursuant to a Rule 10b5-1 Trading Plan. The purchase and sale reported on this Form 4 was effective pursuant to a Rule 10b5-1 Trading Plan adopted by the reporting person's wife on 6/27/2012.