Aim: To fight overweight and obesity in childhood, this study proposes an additional physical activity (PA) in young children aged 6-10 years. The objective was to evaluate the effect of school-based PA on the body composition according to body mass index (BMI) categories (nonobese vs. obese) and gender.Methods: This 6-month study examined the effect of this intervention on body composition in 425 children in 14 primary schools (2 weekly PA sessions of 1 h each) compared to 5 control schools.Adiposity indices were evaluated or calculated: BMI, BMI z-score, waist circumference, sum of skinfolds and fat-free mass.Results: No difference in the prevalence of obesity and anthropometric characteristics was found between the intervention and control groups at baseline. In girls, PA intervention had significant effect on all anthropometric variables (p < 0.05 to p < 0.001), except on BMI. In contrast, in boys only BMI z-score (p < 0.001) and fat-free mass (p < 0.001) were affected.Conclusions: Six months of preventive PA intervention offer an effective means to improve body composition in obese children. The pattern of response related to PA was similar between girls and boys. In contrast, the pattern was different according to BMI category, with a higher response in obese than nonobese children.