<PAGE>

                                                                     EXHIBIT 3.1

                       CERTIFICATE OF LIMITED PARTNERSHIP
                                       OF
                         NORTHERN BORDER PARTNERS, L.P.

      This Certificate of Limited Partnership has been duly executed, is being
filed pursuant to 6 Del. C. Section 17-201, and shall be effective immediately
upon filing.

      1.    The name of this limited partnership is "Northern Border Partners,
            L.P."

      2.    The address of the registered office is:

            Corporation Trust Company
            1209 Orange Street
            Wilmington, New Castle County, Delaware  19801

      The name and address of the registered agent for service of process are:

            The Corporation Trust Company
            Corporation Trust Center
            1209 Orange Street
            Wilmington, New Castle County, Delaware  19801

      3.    The name and the business address of each general partner are:

            Northern Plains Natural                      Pan Border Gas
            Gas Company                                  Company
            1111 South 103 Street                        5400 Westheimer Court
            Omaha, Nebraska 68124                        Houston, Texas 77056

            Northwest Border Pipeline Company
            One Williams Center
            East Second Street
            Tulsa, Oklahoma 74172

                                                       NORTHERN PLAINS NATURAL
                                                       GAS COMPANY
                                                       General Partner

                                                       By: /s/ Gary A. McConnell
                                                           ---------------------
                                                           Gary A. McConnell
                                                           Vice President

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                                                       PAN BORDER GAS COMPANY
                                                       General Partner

                                                       By: /s/ George L.Mazanec
                                                           ---------------------
                                                           George L.Mazanec
                                                           Vice President

                                                       NORTHWEST BORDER PIPELINE
                                                       COMPANY
                                                       General Partner

                                                       By: /s/ G. L. Best
                                                           ---------------------
                                                           G. L. Best
                                                           Vice President

                                                       Date: July 12, 1993

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                                                           STATE OF DELAWARE
                                                          SECRETARY OF STATE
                                                       DIVISION OF CORPORATIONS
                                                       FILED 09:00 AM 02/27/2001
                                                          010101868 - 234348O

                            CERTIFICATE OF AMENDMENT

                                       TO

                       CERTIFICATE OF LIMITED PARTNERSHIP

                                       OF

                         NORTHERN BORDER PARTNERS, L.P.

      Northern Border Partners, L.P. (hereinafter called the "partnership"), a
limited partnership organized under the Delaware Revised Uniform Limited
Partnership Act (the "Act"), for the purpose of amending Certificate of Limited
Partnership filed with the office of the Secretary of State of Delaware on July
13,1993, hereby certifies that:

      1. The name of the limited partnership is Northern Border Partners, L.P.

      2. Pursuant to the provisions of Section 17-202, Title 6, Delaware Code,
the amendment to the Certificate of Limited partnership effected by this
Certificate of Amendment is to change the address of the registered office of
the partnership in the State of Delaware to 9 East Loockerman Street, Dover,
Delaware 19901, and to change the name of the registered agent of the
partnership in the State of Delaware at the said address to National Registered
Agents, Inc.

      The undersigned, a general partner of the partnership, executes this
Certificate of Amendment on February 16, 2001.

                                          Northern Plains Natural Gas Company
                                          General Partner

                                          /s/ Geneva K. Holland
                                          --------------------------------------
                                          Geneva K. Holland, Assistant Secretary

<PAGE>

                            CERTIFICATE OF AMENDMENT

                                       TO

                       CERTIFICATE OF LIMITED PARTNERSHIP

                                       OF

                          NORTHERN BORDER PARTNERS, LP.

      NORTHERN BORDER PARTNERS, LP. (hereinafter called the "partnership"), a
limited partnership organized under the Delaware Revised Uniform Limited
Partnership Act (the "Act"), for the purpose of amending the Certificate of
Limited Partnership filed with the office of the Secretary of State of Delaware
on July 13, 1993, hereby certifies that:

      1. The name of the limited partnership is Northern Border Partners, LP.

      2. Pursuant to provisions of Section 17-202, Title 6, Delaware Code, the
Certificate of Limited Partnership is amended as follows:

                The name and business address of each general partner are:

                Northern Plains Natural Gas Company
                13710 FNB Parkway
                Omaha, NE 68154-5200

                Northwest Border Pipeline Company
                c/o TransCanada PipeLines Limited
                450 - 1st Street S.W.
                Calgary, Alberta
                T2P 5H1

                Pan Border Gas Company
                13710 FNB Parkway
                Omaha, NE 68154-5200

      The undersigned, an authorized officer of a general partner of the
partnership, executed this Certificate of Amendment on May 20, 2003.

                                           NORTHERN PLAINS NATURAL GAS
                                           COMPANY, General Partner

                                           /s/ Lori Pinder-Metz
                                           -------------------------------------
                                           Lori Pinder-Metz, Assistant Secretary