Abstract Background The HEALTHY study was designed to respond to the alarming trends in increasing rates of overweight, obesity, and type 2 diabetes mellitus in youth. The objective of this analysis was to examine the effects of the HEALTHY study on student self-reported dietary intakes (energy, macronutrients and grams consumed of selected food groups). Methods HEALTHY was a cluster-randomized study in 42 public middle schools. Students, n = 3908, self-reported dietary intake using the Block Kids Questionnaire. General linear mixed models were used to analyze differences in dietary intake at the end of the study between intervention and control schools. Results The reported average daily fruit consumption was 10% higher at the end of the study in the intervention schools than in the control schools (138 g or approximately 2 servings versus 122 g, respectively, p = 0.0016). The reported water intake was approximately 2 fluid ounces higher in the intervention schools than in the control (483 g versus 429 g respectively; p = 0.008). There were no significant differences between intervention and control for mean intakes of energy, macronutrients, fiber, grains, vegetables, legumes, sweets, sweetened beverages, and higher- or lower-fat milk consumption. Conclusion The HEALTHY study, a five-semester middle school-based intervention program that integrated multiple components in nutrition, physical education, behavior change, and social marketing-based communications, resulted in significant changes to student's reported fruit and water intake. Subsequent interventions need to go beyond the school environment to change diet behaviors that may affect weight status of children. Clinical Trials Registration NCT00458029