<PAGE>

                                                                     EXHIBIT 3.1

                            CERTIFICATE OF AMENDMENT
                                       OF
                          CERTIFICATE OF INCORPORATION
                                       OF
                                ENDOLOGIX, INC.,
                             A DELAWARE CORPORATION

      ENDOLOGIX, INC., a corporation organized and existing under and by virtue
of the Delaware General Corporation Law (the "Corporation"), does hereby
certify:

      FIRST: At a meeting of the Board of Directors of the Corporation
resolutions were duly adopted proposing and declaring advisable the following
amendment to the Certificate of Incorporation of the Corporation, directing that
said amendment be submitted to the stockholders of the Corporation for
consideration thereof. The resolution setting forth the proposed amendment is as
follows:

            RESOLVED, that Article IV, Section (A) of the Certificate of
      Incorporation is hereby amended and restated to read in full as follows:

                                   "ARTICLE IV

            (A) Classes of Stock. This corporation is authorized to issue two
      classes of stock, to be designated, respectively, "Common Stock" and
      "Preferred Stock." The total number of shares that this corporation is
      authorized to issue is sixty-five million (65,000,000). The number of
      shares of Preferred Stock authorized to be issued is five million
      (5,000,000), par value $0.001 per share. The number of shares of Common
      Stock authorized to be issued is sixty million (60,000,000), par value
      $0.001 per share. The shares of Preferred Stock may be issued from time to
      time in one or more series. The Board of Directors of this corporation
      (the "Board of Directors") is expressly authorized to provide for the
      issue of all or any of the remaining shares of the Preferred Stock in one
      or more series, and to fix the number of shares and to determine or alter
      for each such series, such voting powers, full or limited, or no voting
      powers, and such designations, preferences, and relative, participating,
      optional, or other rights and such qualifications, limitations or
      restrictions thereof, as shall be stated and expressed in the resolution
      or resolutions adopted by the Board of Directors providing for the issue
      of such shares and as may be permitted by the General Corporation Law of
      the State of Delaware. Subject to compliance with applicable protective
      voting rights which have been granted to the Preferred Stock or series
      thereof in Certificates of Designation or the corporation's Certificate of
      Incorporation ("Protective Provisions"), but notwithstanding any other
      rights of the Preferred Stock or any series thereof, the rights,
      privileges, preferences and restrictions of any such additional series may
      be subordinated to, pari passu with (including, without limitation,
      inclusion in provisions with respect to liquidation and acquisition
      preferences, redemption and/or approval of matters by vote or written
      consent), or senior to any of those of any present or future class or
      series of Preferred or Common Stock. Subject to compliance with applicable
      Protective Provisions, the

<PAGE>

      Board of Directors is also expressly authorized to increase or decrease
      (but not below the number of shares of such series then outstanding) the
      number of shares of any series subsequent to the issue of shares of that
      series. In case the number of shares of any such series shall be so
      decreased, the shares constituting such decrease shall resume the status
      they had prior to the adoption of the resolution originally fixing the
      number of shares of such series."

      SECOND: That thereafter, pursuant to a resolution of the Board of
Directors, the Annual Meeting of the Stockholders of the Corporation was duly
called and held, upon notice in accordance with Section 222 of the Delaware
General Corporation Law, at which meeting the necessary number of shares as
required by statute were voted in favor of this amendment of the Certificate of
Incorporation.

      THIRD: The amendment of the Certificate of Incorporation herein certified
has been duly adopted in accordance with the provisions of Section 242 of the
General Corporation Law of the State of Delaware.

                            [Signature Page Follows]

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<PAGE>

      IN WITNESS WHEREOF, Endologix, Inc. has caused this Certificate of
Amendment of Certificate of Incorporation to be signed by the undersigned, and
the undersigned has executed this certificate and affirms the foregoing as true
and under penalty of perjury this 23rd day of May, 2006.

                                         /s/ Paul McCormick
                                         --------------------------------------
                                         Paul McCormick,
                                         President and Chief Executive Officer

                                       3
<PAGE>

                            CERTIFICATE OF AMENDMENT
                                       OF
                          CERTIFICATE OF INCORPORATION
                                       OF
                                ENDOLOGIX, INC.,
                             A DELAWARE CORPORATION


         ENDOLOGIX, INC., a Delaware corporation organized and existing under
and by virtue of the Delaware General Corporation Law (the "Corporation"), does
hereby certify:

         FIRST: The Board of Directors of the Corporation, by unanimous written
consent, duly adopted resolutions proposing and declaring advisable the
following amendment to the Certificate of Incorporation of the Corporation,
directing that said amendment be submitted to the stockholders of the
Corporation for consideration thereof. The resolution setting forth the proposed
amendment is as follows:

                  RESOLVED, that Article IV, Section (A) of the Certificate of
         Incorporation is hereby amended to read in full as follows:

                                   "ARTICLE IV

                  (A) Classes of Stock. This corporation is authorized to issue
         two classes of stock, to be designated, respectively, "Common Stock"
         and "Preferred Stock." The total number of shares that this corporation
         is authorized to issue is fifty-five million (55,000,000). The number
         of shares of Preferred Stock authorized to be issued is five million
         (5,000,000), par value $0.001 per share. The number of shares of Common
         Stock authorized to be issued is fifty million (50,000,000), par value
         $0.001 per share. The shares of Preferred Stock may be issued from time
         to time in one or more series. The Board of Directors of this
         corporation (the "Board of Directors") is expressly authorized to
         provide for the issue of all or any of the remaining shares of the
         Preferred Stock in one or more series, and to fix the number of shares
         and to determine or alter for each such series, such voting powers,
         full or limited, or no voting powers, and such designations,
         preferences, and relative, participating, optional, or other rights and
         such qualifications, limitations or restrictions thereof, as shall be
         stated and expressed in the resolution or resolutions adopted by the
         Board of Directors providing for the issue of such shares and as may be
         permitted by the General Corporation Law of the State of Delaware.
         Subject to compliance with applicable protective voting rights which
         have been granted to the Preferred Stock or series thereof in
         Certificates of Designation or the corporation's Certificate of
         Incorporation ("Protective Provisions"), but notwithstanding any other
         rights of the Preferred Stock or any series thereof, the rights,
         privileges, preferences and restrictions of any such additional series
         may be subordinated to, pari passu with (including, without limitation,
         inclusion in provisions with respect to liquidation and acquisition
         preferences, redemption and/or approval of matters by vote or written
         consent), or senior to any of those of any present or future class or
         series of Preferred or Common Stock. Subject to compliance with
         applicable Protective Provisions, the Board of Directors is also
         expressly authorized to increase or decrease (but not below

                                       4
<PAGE>

         the number of shares of such series then outstanding) the number of
         shares of any series subsequent to the issue of shares of that series.
         In case the number of shares of any such series shall be so decreased,
         the shares constituting such decrease shall resume the status they had
         prior to the adoption of the resolution originally fixing the number of
         shares of such series."

         SECOND: The amendment of the Certificate of Incorporation herein
certified has been duly adopted in accordance with the provisions of Section 242
of the General Corporation Law of the State of Delaware.


                            [Signature page follows]


                                       5
<PAGE>

         IN WITNESS WHEREOF, ENDOLOGIX, INC. has caused this Certificate of
Amendment to be signed by its duly authorized Chief Financial Officer this 28th
day of October, 2003.


                                           /s/ David M. Richards
                                           -------------------------------------
                                           David M. Richards,
                                           Chief Financial Officer


                                       6
<PAGE>

                            CERTIFICATE OF AMENDMENT
                                     OF THE
                          CERTIFICATE OF INCORPORATION
                                       OF
                         RADIANCE MEDICAL SYSTEMS, INC.,
                             A DELAWARE CORPORATION


         RADIANCE MEDICAL SYSTEMS, INC., a Delaware corporation organized and
existing under and by virtue of the Delaware General Corporation Law (the
"Corporation"), does hereby certify:

         FIRST: The Board of Directors of the Corporation, by unanimous written
consent, duly adopted resolutions proposing and declaring advisable the
following amendment to the Certificate of Incorporation of the Corporation,
directing that said amendment be submitted to the stockholders of the
Corporation for consideration thereof. The resolution setting forth the proposed
amendment is as follows:

                  RESOLVED, that Article I of the Certificate of Incorporation
         is hereby amended to read in full as follows:

                                   "ARTICLE I

                  The name of the corporation is Endologix, Inc."

         SECOND: That thereafter, the holders of the necessary number of shares
of capital stock of the Corporation gave their written consent in favor of the
foregoing amendment in accordance with the provisions of Section 228 of the
Delaware General Corporation Law.

         THIRD: That said amendment was duly adopted in accordance with the
provisions of Section 242 of the Delaware General Corporation Law of the State
of Delaware.


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<PAGE>

         IN WITNESS WHEREOF, RADIANCE MEDICAL SYSTEMS, INC. has caused this
Certificate of Amendment to be signed by its duly authorized Chief Financial
Officer this 31st day of May, 2002.


                                           /s/ David M. Richards
                                           -------------------------------------
                                           David M. Richards,
                                           Chief Financial Officer


                                       8
<PAGE>

                                    RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                         RADIANCE MEDICAL SYSTEMS, INC.

                    (PURSUANT TO SECTIONS 242 AND 245 OF THE
                GENERAL CORPORATION LAW OF THE STATE OF DELAWARE)

         Radiance Medical Systems, Inc., a corporation organized and existing
under and by virtue of the provisions of the General Corporation Law of the
State of Delaware (the "General Corporation Law").

         DOES HEREBY CERTIFY:

         FIRST: That this corporation was originally incorporated on June 2,
1993, pursuant to the General Corporation Law, under the name of Endosonics
Acquisition Corp.

         SECOND: That this Restated Certificate of Incorporation restates and
integrates and does not further amend the Certificate of Incorporation of this
corporation as theretofore amended and supplemented, and there is no discrepancy
between those provisions and the provisions of this Restated Certificate of
Incorporation.

         THIRD: That the Restated Certificate of Incorporation of this
corporation, as restated, is as follows:

                                   ARTICLE I

         The name of this corporation is Radiance Medical Systems, Inc.

                                   ARTICLE II

         The address of the registered office of this corporation in the State
of Delaware is 2711 Centreville Road, Suite 400, Wilmington, Delaware, 19808
County of New Castle. The name of its registered agent at such address is The
Prentice-Hall Corporation System, Inc.

                                  ARTICLE III

         The nature of the business or purposes to be conducted or promoted is
to engage in any lawful act or activity for which corporations may be organized
under the General Corporation Law of Delaware.

                                   ARTICLE IV

         (A) Classes of Stock. This corporation is authorized to issue two
classes of stock, to be designated, respectively, "Common Stock" and "Preferred
Stock." The total number of shares that this corporation is authorized to issue
is thirty-five million (35,000,000). The number of shares of Preferred Stock
authorized to be issued is five million (5,000,000), par value


                                       9
<PAGE>

$0.001 per share. The number of shares of Common Stock authorized to be issued
is thirty million (30,000,000), par value $0.001 per share. The shares of
Preferred Stock may be issued from time to time in one or more series. The Board
of Directors of this corporation (the "Board of Directors") is expressly
authorized to provide for the issue of all or any of the remaining shares of the
Preferred Stock in one or more series, and to fix the number of shares and to
determine or alter for each such series, such voting powers, full or limited, or
no voting powers, and such designations, preferences, and relative,
participating, optional, or other rights and such qualifications, limitations or
restrictions thereof, as shall be stated and expressed in the resolution or
resolutions adopted by the Board of Directors providing for the issue of such
shares and as may be permitted by the General Corporation Law of the State of
Delaware. Subject to compliance with applicable protective voting rights which
have been granted to the Preferred Stock or series thereof in Certificates of
Designation or the corporation's Certificate of Incorporation ("Protective
Provisions"), but notwithstanding any other rights of the Preferred Stock or any
series thereof, the rights, privileges, preferences and restrictions of any such
additional series may be subordinated to, pari passu with (including, without
limitation, inclusion in provisions with respect to liquidation and acquisition
preferences, redemption and/or approval of matters by vote or written consent),
or senior to any of those of any present or future class or series of Preferred
or Common Stock. Subject to compliance with applicable Protective Provisions,
the Board of Directors is also expressly authorized to increase or decrease (but
not below the number of shares of such series then outstanding) the number of
shares of any series subsequent to the issue of shares of that series. In case
the number of shares of any such series shall be so decreased, the shares
constituting such decrease shall resume the status they had prior to the
adoption of the resolution originally fixing the number of shares of such
series.

         (B) Common Stock.

         1. Dividend Rights. Subject to the prior rights of holders of all
classes of stock at the time outstanding having prior rights as to dividends,
the holders of the Common Stock shall be entitled to receive, when and as
declared by the Board of Directors, out of any assets of this corporation
legally available therefor, such dividends as may be declared from time to time
by the Board of Directors.

         2. Liquidation Rights. Upon the liquidation, dissolution or winding up
of this corporation, the assets of this corporation shall be distributed among
the holders of Common Stock pro rata based on the number of shares of Common
Stock held by each.

         3. Redemption. The Common Stock is not redeemable.

         4. Voting Rights. The holder of each share of Common Stock shall have
the right to one vote, and shall be entitled to notice of any stockholders'
meeting in accordance with the Bylaws of this corporation, and shall be entitled
to vote upon such matters and in such manner as may be provided by law.

                                   ARTICLE V

         A director of this corporation shall not be personally liable to this
corporation or its stockholders for monetary damages for breach of fiduciary
duty as a director, except for liability (i) for any breach of the director's
duty of loyalty to this corporation or its stockholders, (ii) for acts or


                                       10
<PAGE>

omissions not in good faith or which involve intentional misconduct or a knowing
violation of law, (iii) under Section 174 of the Delaware General Corporation
Law, or (iv) for any transaction from which the director derived any improper
personal benefit. If the Delaware General Corporation Law is amended after
approval by the stockholders of this Article to authorize corporation action
further eliminating or limiting the personal liability of directors, then the
liability of a director of this corporation shall be eliminated or limited to
the fullest extent permitted by the Delaware General Corporation Law, as so
amended.

         Any repeal or modification of the foregoing paragraph by the
stockholders of this corporation shall not adversely affect any right or
protection of a director of this corporation existing at the time of such repeal
or modification.

                                   ARTICLE VI

         This corporation reserves the right to amend, alter, change or repeal
any provision contained in this Amended and Restated Certificate of
Incorporation, in the manner now or hereafter prescribed by statute, and all
rights conferred upon stockholders herein are granted to this reservation.

                                  ARTICLE VII

         The Board of Directors may from time to time make, amend, supplement or
repeal the Bylaws; provided, however, that the stockholders may change or repeal
any Bylaw adopted by the Board of Directors; and provided, further, that no
amendment or supplement to the Bylaws adopted by the Board of Directors shall
vary or conflict with any amendment or supplement adopted by the stockholders.

                                  ARTICLE VIII

         The number of directors of this corporation shall be fixed from time to
time by a bylaw or amendment thereof duly adopted by the Board of Directors or
by the stockholders. The current Board of Directors shall be divided into three
(3) classes, as nearly equal in number as possible, designated Class I, Class II
and Class III. The number of directors constituting each Class shall be fixed
from time to time by a resolution duly adopted by the Board of Directors. Class
I directors shall hold office for an initial term expiring at the annual meeting
of stockholders in 1999. Class II directors shall hold office for an initial
term expiring at the annual meeting of stockholders in 2000, and Class III
directors shall hold office for a term expiring at the annual meeting of
stockholders in 2001. At each annual meeting of stockholders held thereafter,
directors shall be elected for a three-year term to succeed the directors of the
Class whose terms then expire.

                                   ARTICLE IX

         Elections of directors need not be by written ballot unless the Bylaws
of this corporation shall so provide.

                                   ARTICLE X

         Meetings of stockholders may be held within or without the State of
Delaware, the Bylaws may provide. The books of this corporation may be kept
(subject to any provision contained in the


                                       11
<PAGE>

statutes) outside the State of Delaware at such place or places as may be
designated from time to time by the Board of Directors or in the Bylaws of this
corporation."

         FOURTH: That the Restated Certificate of Incorporation was duly adopted
by the board of directors without a vote of the stockholders in accordance with
Section 245(b) of the General Corporation Law.

         IN WITNESS WHEREOF, this Restated Certificate of Incorporation has been
signed by the Vice President, Finance and Administration, Chief Financial
Officer as of March 12, 2001.


                                              /s/ Stephen R. Kroll
                                              ----------------------------------
                                              Stephen R. Kroll
                                              Vice President, Finance and
                                              Administration, Chief Financial
                                              Officer and Secretary


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