We studied the effect in children of an exercise intervention program on fracture rates and skeletal traits. Fractures were registered for 5 years in a population-based prospective controlled exercise intervention study that included children aged 6-9 years at study start, 446 boys and 362 girls in the intervention group and 807 boys and 780 girls in the control group. Intervention subjects received 40 min/school day of physical education and controls, 60 min/week. In 73 boys and 48 girls in the intervention group and 52 boys and 48 girls in the control group, bone mineral density (BMD, g/cm(2)) and bone area (mm(2)) were followed annually by dual-energy X-ray absorptiometry, after which annual changes were calculated. At follow-up we also assessed trabecular and cortical volumetric BMD (g/cm(3)) and bone structure by peripheral computed tomography in the tibia and radius. There were 20.0 fractures/1,000 person-years in the intervention group and 18.5 fractures/1,000 person-years in the control group, resulting in a rate ratio of 1.08 (0.79-1.47) (mean and 95 % CI). The gain in spine BMD was higher in both girls (difference 0.01 g/cm(2), 0.005-0.019) and boys (difference 0.01 g/cm(2), 0.001-0.008) in the intervention group. Intervention girls also had higher gain in femoral neck area (difference 0.04 mm(2), 0.005-0.083) and at follow-up larger tibial bone mineral content (difference 0.18 g, 0.015-0.35), larger tibial cortical area (difference 17 mm(2), 2.4-31.3), and larger radial cross-sectional area (difference 11.0 mm(2), 0.63-21.40). As increased exercise improves bone mass and in girls bone size without affecting fracture risk, society ought to encourage exercise during growth.