Objective. This paper describes the rationale, design, and methods of a two-year randomized controlled trial conducted to evaluate the effectiveness of an environmental intervention in 27 elementary schools in Mexico City. Materials and methods. There were two units of analysis, school level addressing changes in elementary public part-time schools, and individual-level addressing behavioral changes in students 9 to 11 years of age. Two intensities of an intervention program were implemented (basic and plus), each containing two intervention components: physical activity and nutrition, supported by a communication/education component. Evaluation of the intervention was carried out during the school cycles 2006-2007 and 2007-2008. Results. Primary outcomes were overweight and obesity prevalence and fitness; environmental and behavioural measures were also examined. Conclusions. This is the first institutional multilevel, multifactorial project, consistent with the best practices available in current literature, carried out in Mexico to prevent childhood obesity in schools.