Many school-based interventions for obesity prevention have been proposed with positive changes in behaviour, but with unsatisfactory results on weight change. The objective was to verify the effectiveness of a combined school- and home-based obesity prevention programme on excessive weight gain in adolescents. Teachers delivered the school-based primary prevention programme to fifth- and sixth-graders (nine schools, forty-eight control classes, forty-nine intervention classes), which included encouraging healthy eating habits and physical activity. A subgroup of overweight or obese adolescents also received a home-based secondary prevention programme delivered by community health professionals. Schools were randomised to intervention or control group. Intent-to-treat analysis used mixed models for repeated continuous measures and considered the cluster effect. The main outcomes were changes in BMI and percentage body fat (%body fat) after one school-year of intervention and follow-up. Against our hypothesis, BMI increased more in the intervention group than in the control group (Δ = 0·3 kg/m2; P = 0·05) with a greater decrease in %body fat among boys (Δ = –0·6 %; P = 0·03) in the control group. The intervention group increased physical activity by 12·5 min per week compared with the control group. Female adolescents in the intervention group ate healthier items more frequently than in the control group. The subgroup that received both the school and home interventions had an increase in %body fat than in the control group (Δ = 0·89 %; P = 0·01). In the present study, a behavioural change led to a small increase in physical activity and healthy eating habits but also to an overall increase in food intake.