OBJECTIVE:To assess the impact of a 6 months nutrition education and physical activity intervention on primary school children through changes in adiposity and physical fitness. DESIGN: Longitudinal school-based controlled evaluation study. SUBJECTS: Children from 1st to 8th grade, 2141 in intervention and 945 in control schools. INTERVENTION: Nutrition education for children and parents, 'healthier' kiosks, 90 min of additional physical activity (PA) weekly, behavioral PA program and active recess. MEASUREMENTS: Adiposity indices (BMI, BMI Z-score, triceps skinfold thickness (TSF), waist circumference and physical fitness (20 m shuttle run test and lower back flexibility). RESULTS: Positive effect on adiposity indices (except TSF) was observed in boys (Po0.001 for BMI Z), while both physical fitness parameters increased significantly in both boys (Po0.001 for each test) and girls (Po0.0001 for each test). A differential effect in BMI Z was observed according to baseline nutritional status. CONCLUSIONS: This intervention showed a robust effect on physical fitness in both genders and decreased adiposity only in boys.