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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
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 oAXwqL9xBL8Uur1Zm4ONog==

<SEC-DOCUMENT>0001142576-08-000014.txt : 20080516
<SEC-HEADER>0001142576-08-000014.hdr.sgml : 20080516
<ACCEPTANCE-DATETIME>20080516140530
ACCESSION NUMBER:		0001142576-08-000014
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20080515
FILED AS OF DATE:		20080516
DATE AS OF CHANGE:		20080516

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			OPTIMER PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0001142576
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				330830300
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		10110 SORRENTO VALLEY ROAD
		STREET 2:		SUITE C
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
		BUSINESS PHONE:		8589090736

	MAIL ADDRESS:	
		STREET 1:		10110 SORRENTO VALLEY ROAD
		STREET 2:		SUITE C
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Poulos Kevin P
		CENTRAL INDEX KEY:			0001380840

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33291
		FILM NUMBER:		08841570

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		8589090736

	MAIL ADDRESS:	
		STREET 1:		10110 SORRENTO VALLEY ROAD
		STREET 2:		SUITE C
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>primary_doc.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2008-05-15</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001380840</rptOwnerCik>
            <rptOwnerName>Poulos Kevin P</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>10110 SORRENTO VALLEY ROAD</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE C</rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Commercial Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2008-05-15</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1257</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>6.035</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2857</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Acquired under the Company's employee stock purchase plan on May 15, 2008.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>John D. Prunty, attorney-in-fact</signatureName>
        <signatureDate>2008-05-16</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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