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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-04-07</periodOfReport>

    <issuer>
        <issuerCik>0000805326</issuerCik>
        <issuerName>EMISPHERE TECHNOLOGIES INC</issuerName>
        <issuerTradingSymbol>EMIS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001194368</rptOwnerCik>
            <rptOwnerName>RACHESKY MARK H MD</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>40 WEST 57TH STREET</rptOwnerStreet1>
            <rptOwnerStreet2>24TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001284082</rptOwnerCik>
            <rptOwnerName>MHR ADVISORS LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>40 WEST 57TH STREET</rptOwnerStreet1>
            <rptOwnerStreet2>24TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001301392</rptOwnerCik>
            <rptOwnerName>MHR Institutional Advisors II LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>40 WEST 57TH STREET</rptOwnerStreet1>
            <rptOwnerStreet2>24TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001354805</rptOwnerCik>
            <rptOwnerName>MHR Capital Partners Master Account LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>40 WEST 57TH STREET</rptOwnerStreet1>
            <rptOwnerStreet2>24TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrant (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-04-07</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>550127</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2006-04-07</value>
            </exerciseDate>
            <expirationDate>
                <value>2011-09-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>550127</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>550127</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>(1)</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrant (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-04-07</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>67084</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>.01</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2006-04-07</value>
            </exerciseDate>
            <expirationDate>
                <value>2011-09-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>67084</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>67084</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>(2)</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes></footnotes>

    <remarks>(1) These securities are held for (i) the account of MHR Capital Partners Master Account LP, an Anguila limited partnership (&quot;Master Account&quot;), as an assignee from MHR Capital Partners (500) LP, a Delaware limited partnership (&quot;Capital Partners (500)&quot;), and (ii) the account of MHR Capital Partners (100) LP, a Delaware limited partnership (&quot;Capital Partners (100)&quot;). MHR Advisors LLC, a Delaware limited liability company (&quot;Advisors&quot;), is the general partner of each of Master Account and Capital Partners (100). Mark H. Rachesky, M.D. (&quot;Dr. Rachesky&quot;) is the managing member of Advisors. In such capacity, Dr. Rachesky may be deemed to be the beneficial owner of the securities held for the account of Master Account and Capital Partners (100). The Reporting Persons may be deemed to beneficially own other securities of the issuer, all as previously reported on the Form 3 dated March 31, 2005, and the Forms 4 dated September 23, 2005 and January 30, 2006.

(2) These securities are held for the accounts of each of Master Account, Capital Partners (100), MHR Institutional Partners II LP (&quot;Institutional Partners II&quot;), a Delaware limited partnership, and MHR Institutional Partners IIA LP (&quot;Institutional Partners IIA&quot;), a Delaware limited partnership. MHR Institutional Advisors II LLC (&quot;Institutional Advisors II&quot;), a Delaware limited liability company, is the general partner of each of Institutional Partners II and Institutional Partners IIA. Dr. Rachesky is the managing member of each of Advisors and Institutional Advisors II. In such capacity, Dr. Rachesky may be deemed to be the beneficial owner of the securities held for the accounts of each of Master Account, Capital Partners (100), Institutional Partners II and Institutional Partners IIA. The Reporting Persons may be deemed to beneficially own other securities of the issuer, all as previously reported on the Form 3 dated March 31, 2005, and the Forms 4 dated September 23, 2005 and January 30, 2006.</remarks>

    <ownerSignature>
        <signatureName>Mark H. Rachesky, MD</signatureName>
        <signatureDate>2006-04-10</signatureDate>
    </ownerSignature>
</ownershipDocument>
