A total of 695 Dutch adolescents participated in a one year cluster randomised controlled trial. In the intervention schools, physical education teachers were instructed to spend 15–30 min of all physical education lessons on strength exercises. Monthly motivational lessons were given to stimulate students to be more physically active. Control schools followed their usual curriculum. The primary outcome measure was body composition assessed by the deuterium dilution technique. Daily physical activity and sedentary behaviour measured by accelerometry served as a secondary outcome. After 1 year, a 1.6% fat mass difference was found in favour of the intervention group. This reflected a 0.9 kg difference in fat free mass and 0.7 kg difference in fat mass. Daily physical activity decreased from baseline to posttest in both groups, but less so in the intervention group. After 1 year, a difference of 0.4% was found for moderate to vigorous physical activities in favour of the intervention group. No differences in sedentary behaviour, or light physical activity were found between groups.