The HEALTHY study was a randomized, controlled, multicenter and middle school-based, multifaceted intervention designed to reduce risk factors for the development of type 2 diabetes. The study randomized 42 middle schools to intervention or control, and followed students from the sixth to the eighth grades. Here we describe the design of the HEALTHY nutrition intervention component that was developed to modify the total school food environment, defined to include the following: federal breakfast, lunch, after school snack and supper programs; a la carte venues, including snack bars and school stores; vending machines; fundraisers; and classroom parties and celebrations. Study staff implemented the intervention using core and toolbox strategies to achieve and maintain the following five intervention goals: (1) lower the average fat content of foods, (2) increase the availability and variety of fruits and vegetables, (3) limit the portion sizes and energy content of dessert and snack foods, (4) eliminate whole and 2% milk and all added sugar beverages, with the exception of low fat or nonfat flavored milk, and limit 100% fruit juice to breakfast in small portions and (5) increase the availability of higher fiber grain-based foods and legumes. Other nutrition intervention component elements were taste tests, cafeteria enhancements, cafeteria line messages and other messages about healthy eating, cafeteria learning laboratory (CLL) activities, twice-yearly training of food service staff, weekly meetings with food service managers, incentives for food service departments, and twice yearly local meetings and three national summits with district food service directors. Strengths of the intervention design were the integration of nutrition with the other HEALTHY intervention components (physical education, behavior change and communications), and the collaboration and rapport between the nutrition intervention study staff members and food service personnel at both school and district levels.