EXHIBIT 3.1



                        AMENDMENT TO THE AMENDED BY-LAWS

                                       OF

                          EMISPHERE TECHNOLOGIES, INC.

                       Effective as of September 23, 2005


      1. Article I, Section 1.5(b) of the Amended By-Laws (the "By-Laws") of
Emisphere Technologies, Inc. (the "Corporation") is hereby amended by deleting
the word "No" at the beginning of the first sentence of the Section and
replacing it with the following:

            "Except as provided in Section 2.12, no"

      2. Article I, Section 1.6(c) of the By-Laws of the Corporation is hereby
amended by deleting the word "Directors" at the beginning of the sentence and
replacing it with the following:

            "Except as provided in Section 2.12, directors"

      3. Article II, Section 2.1 of the By-Laws of the Corporation is hereby
amended by deleting the word "changed" in the third line and replacing it with
the word "decreased," and by adding the following before the period at the end
of the first sentence:

            "; provided, however, that such number may only be increased upon
      the unanimous vote or unanimous written consent of the Board of Directors"

      4. Article II, Section 2.2 of the By-Laws of the Corporation is hereby
amended by adding the following after the last sentence:

            "Notwithstanding anything contained herein to the contrary, any
      vacancy on the Board of Directors created as a result of the resignation,
      removal or other discontinuation of service as a member of the Board of
      Directors of the director elected to the Board of Directors after being
      nominated solely by MHR Fund Management LLC or any of its affiliates
      (collectively, "MHR" and such nominee the "MHR Nominee") shall be filled
      by an individual who shall have been (i) designated by the MHR Nominee
      prior to the effectiveness of such vacancy, other than in the case of
      removal of the MHR Nominee for cause, or (ii) nominated or approved in
      writing by both a majority of the Board of Directors and MHR, in the case
      of removal of the MHR Nominee for cause; provided, however, that the
      Mutual Director (as defined in Section 2.12 hereof) shall only be replaced
      by an individual who shall have been nominated or approved in writing by
      both a majority of the Board of Directors and MHR."


      5. Article II, Section 2.3 of the By-Laws of the Corporation is hereby
amended by deleting such section in its entirety and replacing it with the
following:

            "Any one or more directors, except for the MHR Nominee and the
      Mutual Director, as the case may be, may be removed, with or without
      cause, by the affirmative vote of the holders of a majority of shares of
      common stock outstanding and entitled to vote at the election of directors
      and the MHR Nominee or the Mutual Director, as the case may be, may be
      removed, with or without cause, by the affirmative vote of the holders of
      at least 85% of the shares of common stock outstanding and entitled to
      vote at the election of directors; provided, however, that the foregoing
      stockholder vote requirement shall be of no further force and effect on or
      after the date that MHR's aggregate shares of Common Stock, warrants to
      purchase shares of Common Stock, or any other equity securities
      convertible into, or exchangeable for, any Common Stock, shall be less
      than two (2) percent of the outstanding Common Stock of the Corporation,
      which outstanding Common Stock shall include all shares of Common Stock,
      warrants to purchase shares of Common Stock whose exercise price is equal
      to or less than the closing price per share of Common Stock on the trading
      date immediately prior to such calculation, or any other equity securities
      convertible into, or exchangeable for, any Common Stock at a conversion
      price or exchange rate, respectively, that is equal to or less than the
      closing price per share of Common Stock on the trading date immediately
      prior to such calculation; provided, further, that any vacancy on the
      Board of Directors created as a result of the resignation, removal or
      other discontinuation of service as a member of the Board of Directors of
      the MHR Nominee shall be filled by an individual who shall have been (i)
      designated by the MHR Nominee prior to the effectiveness of such vacancy,
      other than in the case of removal of the MHR Nominee for cause, or (ii)
      nominated or approved in writing by both a majority of the Board of
      Directors and MHR, in the case of removal of the MHR Nominee for cause;
      provided, further, that the Mutual Director shall only be replaced by an
      individual who shall have been nominated or approved in writing by both a
      majority of the Board of Directors and MHR."

      6. Article II, Section 2.4 of the By-Laws of the Corporation is hereby
amended by adding the following before the period at the end of the second
sentence:

            ", except that notice is required to be given, according to the
      procedures specified in Section 2.5, to the MHR Observer (as defined in
      Section 2.12 hereof)"

      7.    Article II, Section 2.5 of the By-Laws of the Corporation is hereby
amended by adding the following after the phrase "to each director..." in the
last sentence:

            "and the MHR Observer"


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      8. Article II, Section 2.7 of the By-Laws of the Corporation is hereby
amended by deleting the comma at the end of the phrase "transaction of business"
in the first sentence and replacing it with the following:

            "; provided, however, that a quorum for the transaction of business
      must include the MHR Nominee and the Mutual Director while in office,"

      9. Article II, Section 2.10 of the By-Laws of the Corporation is hereby
amended by adding the following clause before the period at the end of the first
sentence:

            "; provided, however, that, to the extent permitted by law or any
      applicable rule or listing standard of any securities exchange or market
      on which any of the Corporation's securities are listed or approved for
      trading, each such committee shall include the MHR Nominee as one of its
      members, unless MHR agrees in writing with respect to any committee that
      this provision will not apply."

      10. Article II of the By-Laws of the Corporation is hereby amended by
adding the following Section 2.12 after Section 2.11:

            "SECTION 2.12 MHR Nominee and Observer; Mutual Director. (a) MHR
      shall have the right to nominate in writing the MHR Nominee for election
      to the Board of Directors; provided, however, that the foregoing right to
      nominate the MHR Nominee for election to the Board of Directors shall be
      of no further force and effect on or after the date that MHR's aggregate
      shares of Common Stock, warrants to purchase shares of Common Stock, or
      any other equity securities convertible into, or exchangeable for, any
      Common Stock, shall be less than two (2) percent of the outstanding Common
      Stock of the Corporation, which outstanding Common Stock shall include all
      shares of Common Stock, warrants to purchase shares of Common Stock whose
      exercise price is equal to or less than the closing price per share of
      Common Stock on the trading date immediately prior to such calculation, or
      any other equity securities convertible into, or exchangeable for, any
      Common Stock at a conversion price or exchange rate, respectively, that is
      equal to or less than the closing price per share of Common Stock on the
      trading date immediately prior to such calculation. To the extent
      permitted by law or any applicable rule or listing standard of any
      securities exchange or market on which any of the Corporation's securities
      are listed or approved for trading, the MHR Nominee shall be a member of
      each committee of the Board of Directors, and the MHR Observer shall be
      entitled to attend meetings of any such committee. In addition, MHR and
      the Board of Directors shall promptly select an independent director
      mutually agreed upon in writing by a majority of the Board of Directors
      and MHR (the "Mutual Director") to be nominated for election to the Board
      of Directors, and the Board of Directors shall elect such Mutual Director
      to the Board of Directors. MHR shall further have the right to select a
      representative


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      (the "MHR Observer"), who shall be permitted to attend all meetings of the
      Board of Directors, including meetings of any committees thereof, solely
      in a non-voting, observer capacity. The MHR Observer shall be entitled to
      receive all notices, written materials and other information (including,
      without limitation, advance notice of any committee meetings and copies of
      meeting minutes) given to directors in connection with such meetings
      contemporaneously with any transmission, circulation or delivery of such
      materials and information to the directors; provided, however, that if the
      Board of Directors, based on the advice of outside legal counsel,
      determines that, with respect to a specific matter to be included on the
      agenda for the next meeting of the Board of Directors or any committee
      thereof, the disclosure of information directly related to such matter
      (the "Privileged Information") to the Investor Observer would adversely
      affect the attorney-client privilege in effect at such time between the
      Board of Directors and its counsel, then the Board of Directors may
      withhold solely the Privileged Information from the Investor Observer and
      shall otherwise permit the Investor Observer to (i) participate in the
      meeting of the Board of Directors or any committee thereof and (ii)
      receive any other information that the Investor Observer would otherwise
      be entitled to receive. If the Corporation proposes to take any action by
      written consent in lieu of a meeting of its Board of Directors or of any
      committee thereof, the Corporation shall give written notice thereof to
      the MHR Observer contemporaneously with any transmission, circulation or
      delivery of such written consent to the directors.

            (b) Except as otherwise required by Delaware law or the Certificate
      of Incorporation, all nominees for election to the Board of Directors
      other than those nominated pursuant to subsection (a) above shall be
      nominated in accordance with Section 2.1 of these By-Laws.

      10. Article VI, Section 6.1 of the By-Laws of the Corporation is hereby
amended by adding the following before the period at the end of the last
sentence:

            "; provided, however, that none of the rights of MHR, including the
      provisions contained in Sections 2.1 through 2.5, 2.7, 2.10, 2.12 or 6.1,
      or any other provisions of the By-Laws that may affect the rights of MHR,
      may be altered, amended or repealed in any way without the unanimous vote
      or unanimous written consent of the Board of Directors or the affirmative
      vote of the holders of at least 85% of the shares of common stock
      outstanding and entitled to vote at the election of directors; provided,
      however, that the foregoing stockholder vote requirement shall be of no
      further force and effect on or after the date that MHR's aggregate shares
      of Common Stock, warrants to purchase shares of Common Stock, or any other
      equity securities convertible into, or exchangeable for, any Common Stock,
      shall be less than two (2) percent of the outstanding Common Stock of the
      Corporation, which outstanding Common Stock shall include all shares of
      Common Stock, warrants to purchase shares of Common Stock


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      whose exercise price is equal to or less than the closing price per share
      of Common Stock on the trading date immediately prior to such calculation,
      or any other equity securities convertible into, or exchangeable for, any
      Common Stock at a conversion price or exchange rate, respectively, that is
      equal to or less than the closing price per share of Common Stock on the
      trading date immediately prior to such calculation. In addition, the Board
      of Directors shall not adopt any resolution setting forth, or call any
      meeting of stockholders for the purpose of approving, an amendment to the
      By-Laws that would affect the rights of MHR, including the provisions
      contained in Sections 2.1 through 2.5, 2.7, 2.10, 2.12 or 6.1, or any
      other provisions of the By-Laws that may affect the rights of MHR, without
      a vote in favor of such resolution by the MHR Nominee; provided, however,
      that the foregoing vote requirement shall be of no further force and
      effect on or after the date that MHR's aggregate shares of Common Stock,
      warrants to purchase shares of Common Stock, or any other equity
      securities convertible into, or exchangeable for, any Common Stock, shall
      be less than two (2) percent of the outstanding Common Stock of the
      Corporation, which outstanding Common Stock shall include all shares of
      Common Stock, warrants to purchase shares of Common Stock whose exercise
      price is equal to or less than the closing price per share of Common Stock
      on the trading date immediately prior to such calculation, or any other
      equity securities convertible into, or exchangeable for, any Common Stock
      at a conversion price or exchange rate, respectively, that is equal to or
      less than the closing price per share of Common Stock on the trading date
      immediately prior to such calculation."


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