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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D. C. 20549

FORM 10-K

(Mark One)

For the fiscal year ended June 25, 2003

OR

For the transition period from              to             

Commission File Number 1-3657

WINN-DIXIE STORES, INC.

(Exact name of registrant as specified in its charter)

(904) 783-5000

(Registrant’s telephone number, including area code)

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  þ  No  ¨

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.  ¨

Indicate by check mark whether the Registrant is an accelerated filer (as defined in Exchange Act Rule 12b-2)  Yes  þ  No  ¨.

The aggregate market value of the common stock held by non-affiliates of the registrant, based upon the closing sale price of common stock on January 8, 2003, as reported on the New York Stock Exchange was approximately $1,262,463,692.

As of August 1, 2003, registrant had outstanding 140,819,913 shares of common stock.

DOCUMENTS INCORPORATED BY REFERENCE:

Portions of the registrant’s Proxy Statement for the 2003 Annual Meeting of Shareholders are incorporated by reference in Part III hereof.

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WINN DIXIE STORES, INC.

ANNUAL REPORT ON FORM 10-K FOR THE YEAR ENDED JUNE 25, 2003

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PART I

General:

Winn-Dixie Stores, Inc. (the “Company”) is a major food and drug retailer operating in 12 states in the southeastern United States and the Bahama Islands. According to published reports of sales at June 25, 2003, the Company is one of the largest food retailers and supermarket chains in the southeastern region of the United States.

As of June 25, 2003, the Company, directly or through subsidiaries, operated 1,073 supermarkets. As of June 25, 2003, 33 of the supermarkets had fuel centers and 44 had separate liquor stores. Supermarkets are generally operated under one of the Company’s two formats: combination food and drug stores or grocery warehouse stores. The Company operates stores under several banners that have strong local ties and brand recognition. The Winn-Dixie, Marketplace, Thriftway and City Markets banners are utilized in the combination food and drug store format. The Save Rite and Sack & Save banners represent the grocery warehouse format.

Store locations:

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Store and Other Data:

Segments:

The Company has determined that its operations are within one reportable segment. Accordingly, financial information on segments is omitted.

Strategy:

The Company’s strategic vision is to be the best supermarket in every neighborhood in which we operate, offering the best value, freshest products and outstanding customer service every day, while enhancing shareholder value. The Company plans to achieve this vision by effectively executing several key initiatives including: aligning stores and customers, strengthening superior customer relationships, leveraging operations and support and improving technology and process.

Marketing:

The Company utilizes all forms of mass media and selected forms of highly targeted media for its retail advertising. The Company also incorporates major sponsorships into the marketing plan, such as sponsorship of the Jacksonville Jaguars, the Tampa Bay Buccaneers, the Super Bowl and others. Marketing campaigns are executed on both a national and local basis and are often tailored to individual markets and customer demographics.

In fiscal 2002, the Customer Reward Card was introduced which generates data on customer buying preferences and enables the Company to better focus marketing programs on customer demands and to target individual customers with special offers.

Other marketing initiatives include acting to ensure that appropriate stores’ merchandising mix includes grocery items, such as specialty lines of produce and meat products, and continuing to remodel certain Winn-Dixie stores. Sixty-two older stores were remodeled last year with improved lighting, a contemporary color palette and attractive interior architectural changes.

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Information Technology:

The Company has made significant investments in technology and information systems in order to drive sales growth, improve operating efficiency and support the overall business strategy. During fiscal year 2003, the Company invested in a new buying and billing system, a perpetual inventory and pricing system, labor management systems, the enterprise data warehouse and continued its development of the Customer Reward Card program.

In 2003, the Company began the process of implementing a labor scheduling system available to store management. The system is intended to enable management to schedule the right associates at the right time of the day in order to best meet the customers’ needs.

In 2003, the Company began to equip the truck fleet with onboard computers that use a Global Positioning System to provide direct communication with drivers. This technology allows the Company to effectively route store deliveries while closely monitoring truck mileage and expenses. When fully implemented next year, the system is expected to reduce driver expenses.

In fiscal 2002, the Company implemented the Customer Reward Card which provides shoppers with ongoing benefits and incentives, while providing us with invaluable data on their buying preferences. That information is used to focus marketing programs and to develop product categories and assortments in each store tailored to the needs of each community. In addition, the Customer Reward Card program strengthens customer loyalty by targeting individual customers with special offers.

In addition, the Company has developed several new online programs that enhance customer service. In fiscal 2003, an online pharmacy program for customers to access the Winn-Dixie pharmacy services was introduced. In fiscal 2002, Party ONline, an online ordering service to assist customers with planning parties during the busy holiday season was introduced. The website also features fresh flowers from FTD, the world’s largest floral company as well as Express Special Purchase (ESP) which provides customers access to thousands of foods and other products not commonly found in local stores.

Competition:

The Company generally competes on a basis of location, product quality, service, price, convenience, product variety and store condition. The number and type of competitors vary by location and competitive position varies according to the individual markets in which the Company operates.

The supermarket industry is highly and increasingly competitive and generally characterized by high inventory turnover and narrow profit margins. The Company competes directly with national, regional and local supermarket chains and independent supermarkets. The Company also competes with non-traditional grocery retailers such as dollar discount stores, drug stores, convenience stores, warehouse club stores, deep discount supercenters and conventional department stores. Beyond grocery retailers, the Company also faces competition from restaurants and fast food chains due to the increasing trend of consumers purchasing and consuming food away from home rather than at home.

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Seasonality:

Due to the influx of winter residents to the Sunbelt, particularly to Florida, and increased purchases of food items for the Thanksgiving and Christmas holiday seasons, the Company usually experiences an increase in sales during the months of November to April each year. Interruptions to the normal tourism pattern may have a significant impact on this seasonal sales increase.

Suppliers and Raw Materials Sources:

The Company receives the products sold in its stores and the raw materials used in its manufacturing operations from a number of sources. The Company is not dependent on a single or relatively few suppliers. The Company believes that its products and raw materials generally are available in sufficient supply to adequately meet customer demand.

Environmental Matters:

The Company is subject to federal, state and local environmental laws that apply to property ownership, property development and its store operations. The Company may be subject to certain environmental regulations regardless of whether it leases or owns the stores or land or whether environmental conditions were created by the Company, the owner or a prior tenant.

The Company believes that compliance with federal, state and local environmental laws and regulations have not had a material effect on its capital expenditures, earnings and competitive position. The Company is not aware of any environmental condition at any of its properties that could be considered material. However, it is possible that the environmental investigations of its properties might not have revealed all potential environmental liabilities or might have underestimated any potential environmental issues. It is also possible that future environmental laws and regulations or new interpretations of existing environmental laws will impose material environmental liabilities on the Company or that current environmental conditions of properties that the Company owns or operates will be affected adversely by hazardous substances associated with other nearby properties or the actions of third parties unrelated to the Company. The costs of defending any future environmental claims, performing any future environmental remediation, satisfying any environmental liabilities, or responding to changed environmental conditions could materially adversely affect the Company’s financial condition and operating results.

Government Regulation:

The Company is subject to regulation by a number of government agencies including, but not limited to, the U.S. Food and Drug Administration, the U.S. Department of Agriculture, the Occupational Safety and Health Administration and other federal, state and local agencies.

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The Company’s stores also are subject to local laws regarding zoning, land use and alcoholic beverage sales. The Company believes that it is in material compliance with these laws and regulations.

Employees:

On June 25, 2003, the Company employed approximately 99,200 associates, of whom approximately 39,900 were employed on a full-time basis and 59,300 on a part-time basis. The Company considers its employee relations to be good. No employees are covered by a collective bargaining agreement.

Trademarks:

The Company has invested significantly in the development and protection of the Winn-Dixie name. The right to use the Winn-Dixie name is considered to be an important asset. The Company also owns approximately 100 other trademarks registered or pending in the United States Patent and Trademark Office. The Company considers certain of its trademarks to be of material importance to its business and actively defends and enforces such trademarks.

Merchandising:

The Company supplies its stores with its own manufactured products and products purchased through outside vendors. The products are delivered through the Company’s distribution centers, manufacturing facilities and outside suppliers or directly from manufacturers.

The Company has developed a line of nearly 3,000 corporate brand products under a variety of brand names including Arrow, Astor, Deep South, Thrifty Maid, Chek and Superbrand. The Company is in the process of consolidating the number of brand names to four: Winn-Dixie, Winn-Dixie Prestige, Thrifty Maid and Chek. The Company’s line of products includes dairy, pasta, cereal, snacks, and peanut butter, as well as other quality products. The Prestige line of products includes an extensive array of ice creams and high quality meats. The Thrifty Maid line of products includes canned fruits and vegetables. The Chek line of products includes carbonated beverages.

Manufacturing:

The principal function of the Company’s manufacturing operations is to purchase, manufacture and process private label merchandise sold in Company stores. As measured by sales dollars, approximately 50% of the Company’s private label merchandise is manufactured in Company plants and the remainder is purchased from third parties.

The Company utilizes its manufacturing operations to produce and sell products on a wholesale basis in order to maximize production capacity. An insignificant portion of sales is derived from this business.

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The Company operated the following manufacturing operations at June 25, 2003:

The ice cream plants are located in facilities that also contain a milk bottling plant. The carbonated beverage plant is located in the same facility as the jam, jellies and condiment plant.

Distribution:

Each of the Company’s retail operating areas is served by a regional distribution center consisting of one or more facilities. The Company has 15 distribution centers (14 in the United States and one in the Bahamas), which collectively provide the majority of all products to the Company’s stores.

Additional Information:

The Company is a Florida corporation that was incorporated in 1928. The corporate headquarters is located at 5050 Edgewood Court, Jacksonville, Florida 32254-3699. The telephone number is 904-783-5000. The Company’s website located at www.winn-dixie.com provides additional information about the Company. The Company makes available through its website, free of charge, Annual Reports on Form 10-K, Quarterly Reports on Form 10-Q and Current Reports on Form 8-K, including any amendments. These forms are available as soon as reasonably practicable after they are filed electronically with the SEC. The website address is included throughout this filing only as a textual reference. The information contained on the Company’s website is not incorporated by reference into this Form 10-K.

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Retail Operations:

The Company conducts its retail operations in 11 owned properties and 1,062 leased properties. Each lease provides for a minimum annual rent and certain of these leases require additional rental payments to the extent sales volumes exceed specified amounts.

Manufacturing and Distribution Operations:

The Company conducts its manufacturing operations in six owned facilities and ten leased facilities. The Company owns four of its distribution centers and leases the eleven.