This non-randomized prospective controlled study evaluates a daily school-based exercise intervention program of 40 min/school day for 1 year in a population-based cohort of 81 boys aged 7–9 years. Controls were 57 age-matched boys assigned to the general school curriculum of 60 min/week. Bone mineral content (BMC; g) and areal bone mineral density (aBMD; g/cm2) were measured with dual X-ray absorptiometry (DXA) of the total body, the third lumbar vertebra (L3) and the femoral neck (FN). Bone width for L3 and FN was calculated from the lumbar spine and hip scan. No differences between the groups were found at baseline in age, anthropometrics or bone parameters. The mean annual gain in L3 BMC was 5.9 percentage points higher (P<0.001), L3 aBMD a mean 2.1 percentage points higher (P=0.01) and L3 width a mean 2.3 percentage points higher (P=0.001) in the cases than in the controls. When all individuals were included in one cohort, the total duration of exercise including both school-based and spare-time training correlated with L3 BMC (r=0.26, P=0.003), L3 aBMD (r=0.18, P=0.04) and L3 width (r=0.24, P=0.006). The study suggests that exercise in pre-pubertal boys influences the accrual of bone mineral and bone width and that a 1-year school-based exercise program confers skeletal benefits, at least in the lumbar spine.