The interplay of physical activity and vitamin D receptor (VDR) gene polymorphism in their effects on bone mineral density (BMD) was studied for 120 Japanese girls aged 18-19 years. BMD at distal radius in the group with the VDR genotype at the Apal site of Aa was significantly higher than that in the aa group, but this association disappeared in a group having the habit of physical activity. The Aa genotype gave a higher BMD than the aa genotype only in the group without the habit of physical activity. The habit of physical activity was associated with a higher BMD only in the aa genotype group. The similar interplay was observed in the VDR genotype at the TaqI site. We thus suggest that physical activity and VDR genotypes affect BMD in independent mechanism to give a saturated level of BMD. Higher dietary calcium intake tended to be associated with higher BMD only in the Aa genotype, suggesting that the calcium intake and VDR genotype affect BMD in a synergistic mechanism.