This study evaluates the effect on the skeleton of physical activity from age 9 to 16. In 42 girls and 44 boys, bone mass and bone size were evaluated longitudinally by dual-energy X-ray absorptiometry (DXA) from ages 13 to 16. Physical activity from ages 9 to 13 was cross-sectionally evaluated at baseline (age 13). Girls with high physical activity from ages 9 to 13 at baseline had higher femoral neck bone mineral content (FN BMC; g) (P = 0.07), higher FN areal bone mineral density (FN aBMD; g/cm2), and higher FN volumetric BMD (FN vBMD; g/cm3) (both P < 0.05) compared with girls of low activity. FN width (cm) and head aBMD (an unloaded region) showed no differences when comparing the two groups. Three years of further high and low activity (from ages 13 to 16) did not yield any increased differences between the two groups. Boys with high physical activity from ages 9 to 13, had at baseline higher FN BMC, FN aBMD, and FN width (all P < 0.05) compared with boys with low activity. FN vBMD and head aBMD showed no differences when comparing the two groups. Three years of further high and low activity did not yield any increased differences between the two groups. We conclude that exercise may yield skeletal benefits before age 13, and that 3 years of continued high or low level activity up to age 16 did not yield any increased differences in bone size or bone mass in either girls or boys.