EXHIBIT 10.1

             AMENDMENT NO. 1 TO THE COMMON STOCK PURCHASE AGREEMENT

                                  July 10, 2006

      This Amendment No. 1 (this "Amendment") to the Common Stock Purchase
Agreement (the "Agreement") dated March 24, 2006, by and between Biotech Shares
Ltd., an entity organized and existing under the laws of the Isle of Man (the
"Investor"), and Idera Pharmaceuticals, Inc., a corporation organized and
existing under the laws of the State of Delaware (the "Company"), is entered
into as of the 10th day of July 2006.

      WHEREAS, under the terms of the Agreement the Company has the right to
sell to the Investor up to $2,500,000 of the Company's Common Stock prior to the
effectiveness of the Pre-Issuance Registration Statement (as such term is
defined in the Agreement);

      WHEREAS, the Company and the Investor have agreed pursuant to an amendment
to the Registration Rights Agreement (as defined in the Agreement) that the
Company shall not be obligated to file the Pre-Issuance Registration Statement
with the United States Securities and Exchange Commission until August 14, 2006;
and

      WHEREAS, the Company desires to sell to the Investor in excess of
$2,500,000 of the Company's Common Stock prior to such date;

      WHEREAS, in order to allow the Company to sell the desired number of
shares of its Common Stock prior to such date, the Company and the Investor
agree that certain terms of the Agreement must be amended.

      NOW, THEREFORE, the Company and the Investor agree as follows:

Amendment to $2,500,000 Purchase Amount Limitation.

1.    The second sentence of Section 3(a) of the Agreement is hereby deleted in
      its entirety and the following is substituted in lieu thereof:

      "(a) If the Purchase Notice involves a Purchase Amount, which when
      aggregated with the Purchase Amount of Common Stock previously sold to the
      Investor hereunder exceeds $3,500,000, the Company shall confirm in such
      Purchase Notice that a registration statement (the "Pre-Issuance
      Registration Statement") covering the resale of the shares of Common Stock
      to be issued on such closing date has been declared and is effective and
      that the certificates representing such shares shall not bear a restricted
      securities legend."

2.    Section 3(d) of the Agreement is hereby deleted in its entirety and the
      following is substituted in lieu thereof:

      "(d) Notwithstanding the foregoing, the Investor shall have no obligation
      hereunder to purchase any shares of Common Stock if the Purchase Amount of
      such shares, when aggregated with the Purchase Amount of Common Stock
      previously sold to the Investor under this Agreement, exceeds $3,500,000
      unless the Pre-Issuance Registration Statement



      has been declared and is effective and the certificates representing such
      shares will not bear a restricted securities legend."

Reverse Split Purchase Price.

In order to reflect the reverse stock split effected on June 30, 2006, Section
3(b) of the Agreement is hereby deleted in its entirety and the following is
substituted in lieu thereof:

      "(b) The number of shares of Common Stock to be issued in connection with
      a Purchase Notice shall be determined by dividing (1) the Purchase Amount
      specified in the Purchase Notice by (ii) the greater of (A) $5.12 and (B)
      80% of the volume-weighted average of the Closing Prices (as defined
      below) of the Common Stock for the five consecutive Trading Days (as
      defined below) immediately preceding the date that the Company sends such
      Purchase Notice to the Investor."

Purchase Notice.

1.    Attached hereto as Exhibit A is a Purchase Notice providing for the sale
      of $3,500,000 of Common Stock to the Investor at a closing to be held on
      July 24, 2006, pursuant to the terms of the Agreement, as amended by this
      Amendment.

2.    The Investor acknowledges the delivery of the Purchase Notice as of the
      date hereof.

Miscellaneous

1.    This Amendment may be executed in identical counterparts, each of which
      shall be deemed an original but all of which shall constitute one and the
      same agreement. This Amendment, once executed by a party, may be delivered
      by facsimile transmission of a copy of this Amendment bearing the
      signature of the party so delivering this Amendment.

2.    Except as expressly modified by or pursuant to this Amendment, the Common
      Stock Purchase Agreement shall remain in full force and effect without any
      other change or modification.



IN WITNESS WHEREOF, the parties have caused this Amendment No. 1 to the
Agreement to be duly executed as of the day and year first above written.

                             COMPANY:

                             IDERA PHARMACEUTICALS, INC.

                             By:         /s/ Sudhir Agrawal
                                 ------------------------
                                 Name:   Sudhir Agrawal
                                 Title:  Chief Executive Officer

                             INVESTOR:

                             BIOTECH SHARES LTD.

                             By:         /s/ Oussama Salam
                                 Name:   Oussama Salam
                                 Title:  Director



                                    Exhibit A

                           IDERA PHARMACEUTICALS, INC.
                               345 VASSAR STREET
                            CAMBRIDGE, MA 02139-4818

                                                                   July 10, 2006

Biotech Shares Ltd.
St. James's Chambers
64A Athol Street
Isle of Man IM1 1JE

         Re:      Purchase Notice

Gentlemen:

         Pursuant to and in accordance with the terms of that certain Common
Stock Purchase Agreement, dated March 24, 2006 (the "PURCHASE AGREEMENT"), as
amended, by and between Biotech Shares Ltd. (the "INVESTOR") and Idera
Pharmaceuticals, Inc. (the "COMPANY"), the Company hereby provides notice (the
"PURCHASE NOTICE") to the Investor that the Company has duly elected to issue
and sell to the Investor, and the Investor is hereby obligated to purchase from
the Company, the number of shares of common stock of the Company, US$0.001 par
value per share (the "COMMON STOCK"), set forth below, on such date and for such
dollar amount as is set forth below (the "DRAWDOWN"):

1.    The number of shares of Common Stock to be issued to the Investor on the
      Drawdown Date (as defined below) to its account with First National Bank
      S.A.L.: 683,593 the "SHARES").

2.    The dollar amount of the Shares: US$3,499,996.16 (the "PURCHASE AMOUNT" or
      "DRAWDOWN AMOUNT").

3.    The closing date for the Drawdown (and the date on which payment of the
      Purchase Amount shall be made to the Company): July 24, 2006 (the
      "DRAWDOWN DATE").

4.    The price per share of the Common Stock used to calculate the number of
      Shares to be issued on the Drawdown Date: US$5.12 per share of Common
      Stock.

      The Company hereby confirms that the Shares and the Drawdown Amount are in
compliance with all of the terms and conditions of the Purchase Agreement.

                             IDERA PHARMACEUTICALS, INC.

                             By:
                                 -------------------------
                                 Name:
                                 Title: