EXHIBIT 10.3 SECOND AMENDMENT TO THE AMENDED AND RESTATED AGREEMENT OF LIMITED PARTNERSHIP OF GREAT LAKES REIT, L.P. This Second Amendment to the Amended and Restated Agreement of Limited Partnership of Great Lakes REIT, L.P. (the "Second Amendment") is made and entered into as of the 10th day of February, 1997 by Great Lakes REIT, Inc., a Maryland corporation ("GLREIT"). RECITALS: WHEREAS, GLREIT is the sole general partner of a Delaware limited partnership known as Great Lakes REIT, L.P. (the "Partnership"), the business and affairs of which are conducted in accordance with the terms and conditions of a certain Agreement of Limited Partnership dated September 27, 1996, as amended and restated by the Amended and Restated Agreement of Limited Partnership dated as of December 19, 1996, and the First Amendment to the Amended and Restated Agreement of Limited Partnership of Great Lakes REIT, L.P. dated February 6, 1997 (collectively the "Partnership Agreement"); and WHEREAS, Section 13.1(b)(ii) of the Partnership Agreement expressly provides, that GLREIT, the general partner of the Partnership shall amend the Partnership Agreement to reflect the admission of Partners in conformance with the Partnership Agreement; and WHEREAS, the certain unitholders of JMG Court Office Center Limited Partnership ("COC"), JMG Elgin Industrial Limited Partnership ("Elgin LP") and the Elgin Industrial Joint Venture ("Elgin JV") listed in Exhibit A attached hereto (the "Accepting Partners") have accepted the Exchange Offer dated January 24, 1997 pursuant to which the Partnership offered Limited Partnership Units in the Partnership in consideration for units in COC, Elgin LP and Elgin JV; and WHEREAS, GLREIT as general partner of the Partnership desires to amend the Partnership Agreement to reflect the addition of the Accepting Partners to the Partnership as new Limited Partners and to revise the percentage interests of the Partners to reflect the new interests; and NOW THEREFORE, the parties hereto hereby agree as follows: 1. The Accepting Partners identified in Exhibit A attached hereto are hereby added to the Partnership as new Limited Partners and the Percentage Interests of the Partners are hereby revised as noted in Exhibit A attached. 2. The date of this Second Amendment shall be the effective date of the transfer to the Partnership of the remainder of the properties owned by GLREIT as of December 31, 1996, so long as GLREIT completes the transfer no later than September 31, 1997. Notwithstanding that title to such assets may remain in the name of GLREIT, so long as such transfer is completed by the date noted above, all of the economic consequences of the operation of such properties shall, subject to the claims and restrictions of any secured lender, benefit and reside with the Partnership for the period from the date of this Second Amendment to the transfer date. 3. Except as set forth above, no other provision of the Partnership Agreement shall be affected, amended or modified except to the extent necessary to conform to the above amendment. Unless defined herein all capitalized terms used in this Second Amendment shall have the definition provided in the Partnership Agreement. 4. This Second Amendment has been proposed by GLREIT, in its capacity as the General Partner of the Partnership in accordance with the provisions of Section 13.1(b)(ii) of the Partnership Agreement. IN WITNESS WHEREOF, the parties hereto have executed this Second Amendment as of the date and year first above written. GREAT LAKES REIT, INC. By: James Hicks ------------------------ James Hicks Its: Vice President EXHIBIT A TO THE AMENDED AND RESTATED AGREEMENT OF LIMITED PARTNERSHIP OF GREAT LAKES REIT, L.P. Effective Date: February 10,1997 Partnership Preferred Percentage Name and Address Capital Contribution Units Units Interest - ---------------- -------------------- ------- ------- -------- GENERAL PARTNER: Great Lakes REIT, Inc. Real estate and cash 2,855,425.5 68,116.7 49.9923% 823 Commerce Drive Oak Brook, IL 60523 LIMITED PARTNERS: GLR No. 3 Cash 881 0 0.0154% 823 Commerce Drive Oak Brook, IL 60523 Great Lakes REIT, Inc. Real estate and cash 2,855,425.5 68,116.7 49.9923% 823 Commerce Drive Oak Brook, IL 60521 JMG COURT OFFICE CENTER LIMITED PARTNERSHIP UNITS OR CASH TO BE EXCHANGED FOR INTERESTS: - -------------------------------------------------------------------------------- Barz, Dale C. 523.150 May, Diane E. 523.150 Beemsterboer, Francine 523.150 Cole, Richard G. Trust 4,185.200 Grodrian, Tim A. 261.575 Guckien, John V. Trust 2,092.600 Hutson, Sandra L. Trust 2,092.600 Janus, Wayne M. Trust 2,092.600 Meulemans, Sandra J. 1,150.930 Milczarek, Alex 2,092.600 Saslow, Judy A. 2,092.600 Shworles, Helen E.D. 2,092.600 Spandikow, Mark S. & Donna 1,046.300 JMG FOX VALLEY LIMITED PARTNERS LIMITED PARTNERS - --------------------------- Bergold, Roy T., Jr. Fox Valley LP Units 1,428.865 Bialek, Thaddeus R. Trust Fox Valley LP Units 1,714.638 Broffman, Morton H. Fox Valley LP Units 1,714.638 Calandra, Patricia M. Fox Valley LP Units 5,715.462 Cascino, Anthony E. Fox Valley LP Units 2,857.731 Clark, W.H. Fox Valley LP Units 5,715.462 DeHaan, Sharon Fox Valley LP Units 1,428.865 Grodrian, Tim A. Fox Valley LP Units 285.773 Hutson, Richard W. Trust Fox Valley LP Units 3,715.050 Kennedy, Walker, Jr. & Diane W. Fox Valley LP Units 857.319 Knowles, Nancy W. Trust Fox Valley LP Units 28,577.308 Krohn, Karen A. Loving Trust Fox Valley LP Units 1,428.865 Lenon, Richard A. Trust Fox Valley LP Units 2,857.731 Mar, Donald Y. & Jana T. Fox Valley LP Units 1,143.092 Moen, Timothy P. Fox Valley LP Units 857.319 Saslow, Judy A. Fox Valley LP Units 4,286.596 Shworles, Helen E.D. Fox Valley LP Units 5,715.462 Slattery, Anastasia M. & William E. Fox Valley LP Units 857.319 Zoldan, Jack S. Fox Valley LP Units 1,428.865 Cole, Richard G. Elgin Indust. JV Units 24,778.969 FCL Mackey Elgin Indust. JV Units 24,050.031