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SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549

FORM 10-K

For the fiscal year ended December 31, 2003

OR

Commission file number 1-14307

GREAT LAKES REIT
(Exact Name of Registrant as Specified in Its Charter)

823 Commerce Drive
Suite 300
Oak Brook, Illinois 60523
(630) 368-2900
(Address and telephone number of principal executive offices)

Securities registered pursuant to Section 12(b) of the Act:

Securities registered pursuant to Section 12(g) of the Act:

None

        Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ý    No o

        Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant's knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. ý

        Indicate by check mark whether the registrant is an accelerated filer (as defined in Rule 12b-2 of the Exchange Act).Yes ý    No o

        As of June 30, 2003, the aggregate market value of common shares of beneficial interest held by non-affiliates of the registrant was $240,913,376. As of March 1, 2004, the aggregate market value of common shares of beneficial interest held by non-affiliates of the registrant was $228,717,136.

        The number of shares of the registrant's common shares of beneficial interest outstanding as of March 1, 2004 was 16,090,628.

GREAT LAKES REIT

Form 10-K Annual Report—2003

        Table of Contents

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PART I

ITEM 1—BUSINESS

General

        Great Lakes REIT, a Maryland real estate investment trust that is the successor to a business that was organized and began operations in 1992 (the "Company"), is a fully integrated, self-administered and self-managed real estate company. As of December 31, 2003, the Company owned and operated 44 properties (the "Properties") in the Chicago, Milwaukee, Detroit, Columbus, Minneapolis, Denver and Cincinnati areas (the "Current Markets"). The Properties contain approximately 5.8 million rentable square feet leased to more than 600 tenants with a weighted average occupancy rate of approximately 78% as of January 1, 2004. The Company has elected to be treated for federal income tax purposes as a real estate investment trust ("REIT"). The Company conducts substantially all of its operations through Great Lakes REIT, L.P. (the "Operating Partnership"), of which the Company is the sole general partner. All references to the "Company," "we," "our" or "us" in this annual report on Form 10-K include the Company and the Operating Partnership unless the context otherwise requires.

Segment Information

        The Company has three reportable segments, distinguished by property type. The property types are office, office service center and medical office properties. Office properties are generally single-story or multi-story buildings used by tenants for office activities. The buildings generally have common area lobbies and other amenities including food service areas, atriums and limited underground parking facilities. Office service center properties generally are one-story buildings with no common areas. Tenant spaces generally have less than 100% office use with the non-office space used for showroom, technical or light storage purposes. Medical office properties are generally connected to or located near hospitals, and the tenants in those properties are primarily health-care providers.

        Revenues by segment expressed as a percentage of total revenues for the years ended December 31, 2003, 2002 and 2001 are as follows:

        For additional financial information about the Company's segments, see Note 10 to the Consolidated Financial Statements included in this report beginning on Page F-1.

Business Strategy

        Historically, the Company's primary business strategy has been to acquire, own and operate well-located, under-performing suburban and medical office properties generally located in certain of the Current Markets at attractive yields and to increase cash flow and property value by implementing a comprehensive operating strategy. The Company's operating strategy includes: (i) investment in value-enhancing renovation and refurbishment programs; (ii) aggressive leasing efforts; (iii) reduction and containment of operating costs; and (iv) a strong emphasis on tenant services and satisfaction. The Company seeks to establish itself as one of the suburban and medical office property owner/operators of choice in the Current Markets and to maximize tenant retention.

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        Historically, the Company has sought to engage in strategic dispositions of select properties. The Company typically seeks to dispose of properties when one or more of the following conditions is present: (i) market prices are at or near replacement cost; (ii) property occupancy is high and there is limited potential to increase cash flow and property value within a reasonable period; (iii) the Company believes that its capital can be re-deployed to investment properties with higher long-term returns; and (iv) ownership of the property is no longer consistent with the Company's business strategy. The Company sold four properties in 2003 aggregating 148,000 square feet resulting in net sales proceeds of $14.6 million. The Company sold four properties in 2002 aggregating 295,000 square feet resulting in net sales proceeds of $33.1 million. In January 2004, the Company signed definitive agreements to sell its portfolio of medical office buildings for a contract price of $69 million and its Minnesota properties for $42 million. The Company has identified certain other assets that it expects to market for sale during 2004 and may consider selling additional properties if market conditions warrant. The Company has not entered into any definitive agreements with respect to any such additional disposition opportunities and there can be no assurances that the Company will consummate any such dispositions.

        In January 2004, the Company entered into a merger agreement with Aslan Realty Partners II, L.P., an affiliate of Transwestern Investment Company, L.L.C ("Transwestern"). Pursuant to the merger agreement, Transwestern agreed to pay $14.98 per share in cash to the Company's common shareholders upon the closing of the merger. The terms of the merger agreement permit the Company to sell certain of its properties, including the portfolio of medical office buildings and its properties located at 2550 University Avenue W., St. Paul, Minnesota and 2221 University Avenue SE, Minneapolis, Minnesota. On March 5, 2004, the Company announced that it had completed the sale of its portfolio of medical office properties for a contract price of $69 million and the sale of its property located at 2550 University Avenue W., St. Paul, Minnesota for a contract price of $35 million.

        As a result, based on the net proceeds from the recently completed sales of the Company's portfolio of medical office buildings and its property located at 2550 University Avenue W., St. Paul, Minnesota, calculated as of March 5, 2004, the Company's common shareholders will be entitled to receive $15.44 per share in cash upon completion of the merger. The merger consideration will be increased automatically if the sale of certain other properties occurs prior to the completion of the merger and those sales provide net proceeds in excess of the applicable agreed value for those properties. The Company has entered into an agreement to sell its property located at 2221 University Avenue SE, Minneapolis, Minnesota to the University of Minnesota for a contract price that would increase the per share contribution payable in the merger by an estimated $0.11 per common share. In addition, the Company has entered into an agreement to sell its property located at 3550 Salt Creek Lane, Arlington Heights, Illinois for a contract price that would increase the per share consideration payable in the merger by an estimated $0.05 per common share. Assuming that the property located at 2221 University Avenue SE, Minneapolis, Minnesota is sold to the University of Minnesota for its contract price and the property located at 3550 Salt Creek Lane, Arlington Heights, Illinois is sold for its contract price, the Company estimates that its common shareholders would be entitled to receive $15.60 per share in cash upon completion of the merger.

        The Company has also entered into a separate agreement with Fortis Asset Management relating to its property located at 2221 University Avenue SE, Minneapolis, Minnesota. That agreement provides for Fortis' purchase of this property in the event the sale of the property to the University of Minnesota is not consummated. If this property is sold to Fortis for the price specified in the contract with Fortis, the per share consideration payable in the merger would be increased by an estimated $0.08 per common share rather than an estimated $0.11 per common share.

        The amount of any increase in the merger consideration will be equal to each common share's ratable portion of the increase, rounded to the nearest whole cent, as described in the merger agreement. The Company will publicly announce any increase in the merger consideration prior to the completion of the merger. However, there can be no assurance that the Company will consummate the sale of its property located at 2221 University Avenue SE, Minneapolis, Minnesota to either the

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University of Minnesota or Fortis or that it will consummate the sale of its property located at 3550 Salt Creek Lane, Arlington Heights, Illinois. In addition, there are no understandings or contracts with respect to any of the other potential sale of properties and there can be no assurance that the Company will sell any of those properties.

        The proposed merger with Transwestern is contingent on shareholder approval and certain other closing conditions but is not contingent on the completion of any of the additional property sales. The proposed sales of individual properties are not contingent on one another or the merger, and each of the proposed property sale transactions is subject to customary closing conditions. The Company expects that the property sale transactions currently under contract will close in April 2004 and expects the merger to close in the April or May of 2004.

Financing Strategy

        The Company seeks to maintain a well-balanced, conservative and flexible capital structure by: (i) currently targeting a ratio of long-term debt to total market capitalization in the range of 40% to 60%; (ii) extending and sequencing the maturity dates of its debt; (iii) focusing on borrowing at fixed rates; (iv) pursuing debt financings and refinancing on a secured basis; and (v) maintaining relatively conservative debt service and fixed charge coverage ratios. In 2002, the Company refinanced its unsecured credit facility with a long-term secured loan. The Company's ratio of long-term debt to total market capitalization may increase as a result of using secured debt in place of unsecured debt. In addition, as discussed under Item 7, "Management's Discussion and Analysis of Financial Condition and Results of Operations," the Company has approximately $41 million of borrowing capacity under two secured loans that it may use for short-term funding of the acquisition of additional properties and for working capital requirements. The Company's debt to total market capitalization ratio (total market capitalization is defined as the total market value of all outstanding common and preferred shares and units of limited partnership interest in the Operating Partnership plus outstanding indebtedness) at December 31, 2003 was 50.2%.

Competition

        All of the Properties are located in competitive markets. The properties with which the Company competes for tenants are generally owned by institutional investors, other REITs or local real estate operators; however, no single competitor or small group of competitors is dominant in any of the Current Markets. In addition, the Company may be competing with other owners and operators that have greater financial resources and more experience than the Company. An increase in the supply and a decrease in the demand for rental properties with characteristics similar to those of the Properties may adversely affect rental rates or the Company's ability to lease space at the Properties or any newly acquired properties. During 2003, vacancy rates in the Current Markets generally trended upward due to both increases in the supply and decreases in demand for office space within the Current Markets. The Company currently expects that such vacancy rate increases will affect the ability of all property owners within the Current Markets, including the Company, to increase rental revenues until such time as vacancy rates begin to trend downward.

Insurance

        The Company carries comprehensive liability, casualty, pollution, extended coverage and rental loss insurance covering all of the Properties, with policy specifications and insured limits that the Company believes are adequate and appropriate under the circumstances. There is, in 2004, no exclusion in the Company's casualty insurance policy for damage caused by acts of terrorism. There are, however, certain types of losses that are not generally insured because they are either uninsurable or not economically feasible to insure. Should an uninsured loss or a loss in excess of insured limits occur, the Company could lose its capital invested in any of the Properties, as well as the anticipated future revenues from such Property and, in the case of recourse debt, the Company would remain obligated

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for any mortgage debt or other financial obligations related to such Property. Any such loss would adversely affect the business, financial condition and results of operations of the Company. Moreover, as the general partner of the Operating Partnership, the Company will generally be liable for any of the Operating Partnership's unsatisfied obligations other than non-recourse obligations. The Company believes that the Properties are adequately insured; however, no assurance can be given that material losses in excess of insurance proceeds will not occur in the future.

Environmental Regulations

        Under various federal, state and local environmental laws, ordinances and regulations, a current or previous owner or operator of real estate may be required to investigate and clean up hazardous or toxic substances or petroleum product releases at such property and may be held liable to a governmental entity or to third parties for property damage and for investigation and clean-up costs incurred by such parties in connection with the contamination. Such laws typically impose clean-up responsibility and liability without regard to whether the owner knew of or caused the presence of the contaminants, and the liability under such laws has been interpreted to be joint and several unless the harm is divisible and there is a reasonable basis for allocation of responsibility. The costs of investigation, remediation or removal of such substances may be substantial, and the presence of such substances, or the failure to properly remediate the contamination on such property, may adversely affect the owner's ability to sell or rent such property or to borrow using such property as collateral. Persons who arrange for the disposal or treatment of hazardous or toxic substances at a disposal or treatment facility also may be liable for the costs of removal or remediation of a release of hazardous or toxic substances at such disposal or treatment facility, whether or not such facility is owned or operated by such person. In addition, some environmental laws create a lien on the contaminated site in favor of the government for damages and costs incurred in connection with the contamination. Finally, the owner of a site may be subject to common law claims by third parties based on damages and costs resulting from environmental contamination emanating from such site. Some or all of these costs may not be covered by pollution insurance.

        During the last eight years, independent environmental consultants have conducted or updated Phase I Environmental Assessments ("Phase I Assessments") at each of the Properties. In addition, a limited-scope Phase II Assessment ("Phase II Assessment") has been conducted at the 2221 University Avenue SE, Minneapolis, Minnesota and 777 East Eisenhower Parkway, Ann Arbor, Michigan properties (the Phase I Assessments and the Phase II Assessments are collectively referred to as the "Environmental Assessments"). The Phase I Assessments have included, among other things, a visual inspection of the Properties and the surrounding area and a review of relevant state, federal and historical documents. Except for the Phase II Assessments and certain limited sampling in connection with underground tank and/or piping removals at the 601 Campus Drive, Arlington Heights, Illinois and 11270 W. Park Place, Milwaukee, Wisconsin properties, no invasive techniques such as soil or groundwater sampling were performed at any of the Properties. The Company's Environmental Assessments of the Properties have not revealed any condition giving rise to an environmental liability that the Company believes would have a material adverse effect on the Company's business, assets or results of operations, taken as a whole, nor is the Company otherwise aware of any such condition. There can be no assurance, however, that the Company's Environmental Assessments would reveal all conditions giving rise to environmental liabilities. Moreover, there can be no assurance that (i) future laws, ordinances or regulations will not impose any material environmental liability or (ii) the current environmental condition of the Properties will not be affected by tenants, the condition of land or operations in the vicinity of the Properties (such as the presence of underground storage tanks), or third parties unrelated to the Company.

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Other Matters

        The Company's operations are not materially dependent on a single or few customers; no single customer accounts for more than 5% of the Company's total revenue. The Company's operations are not subject to significant seasonal fluctuations. As of December 31, 2003, the Company employed 106 persons, none of whom is represented by a collective bargaining unit.

        For additional information about the Company's investments and operations, see Item 7, "Management's Discussion and Analysis of Financial Condition and Results of Operations," and Item 8, "Financial Statements and Supplementary Data." For additional information about the Company's business segments, see Item 8, "Financial Statements and Supplementary Data."

Available Information

        The Company files annual, quarterly and special reports, proxy statements and other information with the Securities and Exchange Commission. Investors can read and copy any materials the Company files with the Securities and Exchange Commission at its Public Reference Room at 450 Fifth Street, N.W., Washington, D.C. 20549. Investors can obtain information about the operations of the Securities and Exchange Commission Public Reference Room by calling the Securities and Exchange Commission at 1-800-SEC-0330. The Securities and Exchange Commission also maintains a Web site that contains information the Company files electronically with the Securities and Exchange Commission, which you can access over the Internet at http://www.sec.gov.

        The Company also makes its annual report on Form 10-K, quarterly reports on Form 10-Q, current reports on Form 8-K and amendments to those reports filed or furnished pursuant to Section 13(a) of the Securities Exchange Act of 1934 (the "Exchange Act") available, free of charge, on its Web site as soon as reasonably practicable after such material is electronically filed with, or furnished to, the Securities and Exchange Commission. The Company's Web site address is http://www.greatlakesreit.com.

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ITEM 2—PROPERTIES

General

        As of December 31, 2003, the Company owned 44 properties containing approximately 5.8 million square feet. The Properties consist primarily of Class A and Class B suburban office and medical office rentable properties, which range in size from approximately 33,000 to 375,000 rentable square feet. The Properties consist of 30 suburban office properties, eight medical office properties, two central business district office buildings, and four office/service centers (generally single-story buildings with both finished office and unfinished storage area). The 44 Properties are located primarily in the suburban areas of Chicago (23), Milwaukee (8), Minneapolis (2), Detroit (5), Columbus (4), Denver (1) and Cincinnati (1). Many of the Properties offer amenities, including indoor and outdoor parking, loading dock facilities, on-site property management, in-house conference facilities and providers of food and beverage service. As discussed in Item 1, "Business," the Company sold its portfolio of medical office buildings and its property located at 2550 University Avenue W, St. Paul, Minnesota in March 2004 and expects that the property sale transaction related to its property located at 2221 University Avenue SE, Minneapolis, Minnesota will close in April 2004.

        As of December 31, 2003, the Properties were leased to more than 600 tenants. No single tenant accounted for more than 3.3% of the aggregate annualized base rent of the Company's portfolio and only 18 tenants individually represented more than 1% of such aggregate annualized base rent.

        The following sets forth information regarding the Company's leases with its largest tenants based upon annualized base rent as of January 1, 2004:

(1)

Weighted average calculation based on aggregate leased square footage for each tenant.

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        The following table sets forth certain of the information as of January 1, 2004 regarding the Properties.

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