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: PARSHALL B LYNNE (Director, COO, Secretary)

Non-Derivative Transactions

Date	Security	Code	Shares	Price	A/D	Holdings After	Ownership
2012-09-04	Common Stock	M	10000	$5.25	Acquired	11985	Direct
2012-09-04	Common Stock	S	10000	$15.001	Disposed	1985	Direct
2012-09-04	Common Stock	M	10000	$5.25	Acquired	10000	Indirect
2012-09-04	Common Stock	S	10000	$15.001	Disposed	0	Indirect
2012-09-04	Common Stock	M	10000	$5.25	Acquired	10000	Indirect
2012-09-04	Common Stock	S	10000	$15.001	Disposed	0	Indirect
2012-09-05	Common Stock	M	2000	$5.25	Acquired	3985	Direct
2012-09-05	Common Stock	S	2000	$15.00	Disposed	1985	Direct
2012-09-06	Common Stock	M	2494	$6.84	Acquired	4479	Direct
2012-09-06	Common Stock	S	2494	$15.035	Disposed	1985	Direct
2012-09-06	Common Stock	M	2506	$5.25	Acquired	4491	Direct
2012-09-06	Common Stock	S	2506	$15.035	Disposed	1985	Direct
2012-09-06	Common Stock	M	5000	$5.25	Acquired	6985	Direct
2012-09-06	Common Stock	S	5000	$15.002	Disposed	1985	Direct
2012-09-06	Common Stock	M	5000	$6.84	Acquired	5000	Indirect
2012-09-06	Common Stock	S	5000	$15.035	Disposed	0	Indirect
2012-09-06	Common Stock	M	5000	$5.25	Acquired	5000	Indirect
2012-09-06	Common Stock	S	5000	$15.002	Disposed	0	Indirect
2012-09-06	Common Stock	M	5000	$6.84	Acquired	5000	Indirect
2012-09-06	Common Stock	S	5000	$15.035	Disposed	0	Indirect
2012-09-06	Common Stock	M	5000	$5.25	Acquired	5000	Indirect
2012-09-06	Common Stock	S	5000	$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	10000	Disposed	2013-01-02	Common Stock (10000)	Direct
2012-09-04	Employee Stock Option (right to buy)	$5.25	M	10000	Disposed	2013-01-02	Common Stock (10000)	Indirect
2012-09-04	Employee Stock Option (right to buy)	$5.25	M	10000	Disposed	2013-01-02	Common Stock (10000)	Indirect
2012-09-05	Employee Stock Option (right to buy)	$5.25	M	2000	Disposed	2013-01-02	Common Stock (2000)	Direct
2012-09-06	Employee Stock Option (right to buy)	$5.25	M	7506	Disposed	2013-01-02	Common Stock (7506)	Direct
2012-09-06	Employee Stock Option (right to uy)	$6.84	M	2494	Disposed	2013-01-01	Common Stock (2494)	Direct
2012-09-06	Employee Stock Option (right to buy)	$5.25	M	5000	Disposed	2013-01-02	Common Stock (5000)	Indirect
2012-09-06	Employee Stock Option (right to buy)	$5.25	M	5000	Disposed	2013-01-02	Common Stock (5000)	Indirect
2012-09-06	Employee Stock Option (right to buy)	$6.84	M	5000	Disposed	2013-01-01	Common Stock (5000)	Indirect
2012-09-06	Employee Stock Option (right to buy)	$6.84	M	5000	Disposed	2013-01-01	Common Stock (5000)	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 1/16/2012.

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 daughter on 1/16/2012.