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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-11-06</periodOfReport>

    <issuer>
        <issuerCik>0000865436</issuerCik>
        <issuerName>WHOLE FOODS MARKET INC</issuerName>
        <issuerTradingSymbol>WFMI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001127599</rptOwnerCik>
            <rptOwnerName>RESTRICTED STOCK SYSTEMS INC/FA</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1></rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAMPLE ADDRESS</rptOwnerCity>
            <rptOwnerState></rptOwnerState>
            <rptOwnerZipCode>123</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isTenPercentOwner>1</isTenPercentOwner>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <transactionDate>
                <value>2009-11-06</value>
                <footnoteId id="F4"/>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>500</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>40600</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F3"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Create a brand new footnote</footnote>
        <footnote id="F2">brand new footdjdjdjdjdjdjdjdj</footnote>
        <footnote id="F3">test test</footnote>
        <footnote id="F4">exercisable each year beginning 10/22/08 in 4</footnote>
    </footnotes>

    <remarks>new remark</remarks>

    <ownerSignature>
        <signatureName>/s/ new person</signatureName>
        <signatureDate>2009-11-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
