<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2013-05-08</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001142576</issuerCik>
        <issuerName>OPTIMER PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>OPTR</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001576510</rptOwnerCik>
            <rptOwnerName>Sirota Eric</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>101 HUDSON STREET</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3501</rptOwnerStreet2>
            <rptOwnerCity>JERSEY CITY</rptOwnerCity>
            <rptOwnerState>NJ</rptOwnerState>
            <rptOwnerZipCode>07302</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Operating Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2129</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Includes 2,129 shares underlying a restricted stock unit that will vest upon the reporting person's separation from the Company.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Meredith Schaum, attorney-in-fact</signatureName>
        <signatureDate>2013-05-13</signatureDate>
    </ownerSignature>
</ownershipDocument>
