-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 GTLZ682KRHMh78IlFejaDYu8TYGC2plV0XzV/S2JOZRB8w4fFl9HxM4MhmXNWJ9b
 n2It0cZJspwUsx9J+B4tYA==

<SEC-DOCUMENT>0001104659-05-053679.txt : 20051109
<SEC-HEADER>0001104659-05-053679.hdr.sgml : 20051109
<ACCEPTANCE-DATETIME>20051108204747
ACCESSION NUMBER:		0001104659-05-053679
CONFORMED SUBMISSION TYPE:	10-Q
PUBLIC DOCUMENT COUNT:		11
CONFORMED PERIOD OF REPORT:	20050930
FILED AS OF DATE:		20051109
DATE AS OF CHANGE:		20051108

FILER:

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ISIS PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0000874015
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				330336973
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		10-Q
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-19125
		FILM NUMBER:		051187668

	BUSINESS ADDRESS:	
		STREET 1:		1896 RUTHERFORD ROAD
		CITY:			CARLSBAD
		STATE:			CA
		ZIP:			92008
		BUSINESS PHONE:		7609319200

	MAIL ADDRESS:	
		STREET 1:		1896 RUTHERFORD ROAD
		CITY:			CARLSBAD
		STATE:			CA
		ZIP:			92008
</SEC-HEADER>
<DOCUMENT>
<TYPE>10-Q
<SEQUENCE>1
<FILENAME>a05-18037_110q.htm
<DESCRIPTION>QUARTERLY REPORT PURSUANT TO SECTIONS 13 OR 15(D)
</DOCUMENT>
<DOCUMENT>
<TYPE>EX-10.1
<SEQUENCE>2
<FILENAME>a05-18037_1ex10d1.htm
<DESCRIPTION>MATERIAL CONTRACTS
</DOCUMENT>
<DOCUMENT>
<TYPE>EX-10.2
<SEQUENCE>3
<FILENAME>a05-18037_1ex10d2.htm
<DESCRIPTION>MATERIAL CONTRACTS
</DOCUMENT>
<DOCUMENT>
<TYPE>EX-10.3
<SEQUENCE>4
<FILENAME>a05-18037_1ex10d3.htm
<DESCRIPTION>MATERIAL CONTRACTS
</DOCUMENT>
<DOCUMENT>
<TYPE>EX-10.4
<SEQUENCE>5
<FILENAME>a05-18037_1ex10d4.htm
<DESCRIPTION>MATERIAL CONTRACTS
</DOCUMENT>
<DOCUMENT>
<TYPE>EX-10.5
<SEQUENCE>6
<FILENAME>a05-18037_1ex10d5.htm
<DESCRIPTION>MATERIAL CONTRACTS
</DOCUMENT>
<DOCUMENT>
<TYPE>EX-31.1
<SEQUENCE>7
<FILENAME>a05-18037_1ex31d1.htm
<DESCRIPTION>302 CERTIFICATION
</DOCUMENT>
<DOCUMENT>
<TYPE>EX-31.2
<SEQUENCE>8
<FILENAME>a05-18037_1ex31d2.htm
<DESCRIPTION>302 CERTIFICATION
</DOCUMENT>
<DOCUMENT>
<TYPE>EX-32.1
<SEQUENCE>9
<FILENAME>a05-18037_1ex32d1.htm
<DESCRIPTION>906 CERTIFICATION
</DOCUMENT>
<DOCUMENT>
<TYPE>GRAPHIC
<SEQUENCE>10
<FILENAME>g180371kki001.jpg
<DESCRIPTION>GRAPHIC
</DOCUMENT>
<DOCUMENT>
<TYPE>GRAPHIC
<SEQUENCE>11
<FILENAME>g180371kki002.gif
<DESCRIPTION>GRAPHIC
</DOCUMENT>
</SUBMISSION>