-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 FYRLF8JWoi4LioDrzibQW/Zn8gdKM3WLQ0pWWAGQtHBvm99JSyFcJKreqXG2XCNk
 qKxIGxlGOc+bFl1Qd6z6tg==

<SEC-DOCUMENT>0001140361-06-017464.txt : 20061205
<SEC-HEADER>0001140361-06-017464.hdr.sgml : 20061205
<ACCEPTANCE-DATETIME>20061205110034
ACCESSION NUMBER:		0001140361-06-017464
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20061201
FILED AS OF DATE:		20061205
DATE AS OF CHANGE:		20061205

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:			SCOON DAVEY
		CENTRAL INDEX KEY:			0001270110

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-14732
		FILM NUMBER:		061256253

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		7816859700

	MAIL ADDRESS:	
		STREET 1:		12 OAK PARK DRIVE
		CITY:			BEDFORD
		STATE:			MA
		ZIP:			01730
</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>2006-12-01</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001270110</rptOwnerCik>
            <rptOwnerName>SCOON DAVEY</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>59.10</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-12-01</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>6128</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2007-12-01</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-12-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>6128</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>6128</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 six thousand one hundred and twenty eight options vest in four equal annual installments, with the first installment vesting on December 1, 2007.</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>2006-12-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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