We investigated the relation between the vitamin D receptor (VDR) genotype and bone mass including the effect of exercise history as a measure of physical activity. BUA (broadband ultrasound attenuation), SOS (speed of sound) and Stiffness index of the calcaneus were measured using an ultrasound bone densitometer in 105 Japanese young adult women (age: mean±SD 20.4±4.1 years, ranged 18–37) by the calcaneal ultra sound measurement to assess bone mass. Physical activity was measured using a questionnaire about exercise and was calculated as exercise hours per week during prepuberty (elementary school), puberty (junior and senior high school) and a current period (from >18 years old). VDR genotype was determined by the BsmI restriction site of the VDR gene. Significant differences were observed in age-adjusted and menarche age-adjusted SOS and Stiffness between BsmI VDR genotypes. We also examined the interaction between VDR genotype and the amount of exercise. The association between ultrasound parameters and exercise hours per week was evaluated with simple regression analysis according to VDR genotype. There was a significant difference in the slope between VDR genotypes in regression analysis of exercise hours per week during senior high school for SOS (P<0.05). Furthermore, we conducted multiple regression analysis to examine the contribution of each factor to ultrasound parameters. VDR genotype was a significant independent variable for SOS (P<0.05). Exercise hours each week during senior high school was a significant independent variable for all ultrasound parameters (all: P<0.001). In conclusion, there was a partial significant relation between VDR genotype and ultrasound parameters, but the exercise hours each week during senior high school was the strongest independent factor for bone mass in young adult Japanese women.