-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
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 R0GI0OMq8V4rZpAV/+GTUA==

<SEC-DOCUMENT>0001140361-06-015909.txt : 20061109
<SEC-HEADER>0001140361-06-015909.hdr.sgml : 20061109
<ACCEPTANCE-DATETIME>20061109171423
ACCESSION NUMBER:		0001140361-06-015909
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20061107
FILED AS OF DATE:		20061109
DATE AS OF CHANGE:		20061109

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ADVANCED MAGNETICS INC
		CENTRAL INDEX KEY:			0000792977
		STANDARD INDUSTRIAL CLASSIFICATION:	IN VITRO & IN VIVO DIAGNOSTIC SUBSTANCES [2835]
		IRS NUMBER:				042742593
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			0930

	BUSINESS ADDRESS:	
		STREET 1:		125 CAMBRIDGEPARK DRIVE, 6TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02140
		BUSINESS PHONE:		6174972070

	MAIL ADDRESS:	
		STREET 1:		125 CAMBRIDGEPARK DRIVE, 6TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02140

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			ZWANZIGER RON
		CENTRAL INDEX KEY:			0001033433

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-14732
		FILM NUMBER:		061203638

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		6179695689

	MAIL ADDRESS:	
		STREET 1:		322 WAVERLY AVE
		CITY:			NEWTON
		STATE:			MA
		ZIP:			02158
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc1.xml
<DESCRIPTION>FORM 4
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-11-07</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000792977</issuerCik>
        <issuerName>ADVANCED MAGNETICS INC</issuerName>
        <issuerTradingSymbol>AMAG</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001033433</rptOwnerCik>
            <rptOwnerName>ZWANZIGER RON</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ADVANCED MAGNETICS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>125 CAMBRIDGEPARK DRIVE, 6TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02140</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>41.16</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-11-07</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>8801</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2007-11-07</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-11-07</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>8801</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>8801</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Grant of stock options pursuant to the Advanced Magnetics, Inc. Amended and Restated 2000 Stock Plan.  These eight thousand eight hundred and one options vest in four equal annual installments, with the first installment vesting on the first anniversary of the date of grant.</footnote>
        <footnote id="F2">The exercise price is reported in column 2.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Joseph L. Farmer, attorney-in-fact</signatureName>
        <signatureDate>2006-11-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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