Aims: The purpose of this study was to investigate interactions of vitamin D receptor gene (VDR) polymorphisms and regular physical exercise on BMD in a four-year randomized, controlled intervention trial in Finnish middle-aged men. Methods: The TaqI, FokI, and ApaI RFLP-markers of the VDR gene were evaluated. BMDs of the lumbar spine (L2–L4), femoral neck, and total proximal femur were measured with a dual-energy X-ray absorptiometry (DXA). Results: In the entire study group, the subjects with the VDR gene TaqI Tt or tt genotype had a greater body height and higher femoral neck BMD values than the TT subjects (p=0.001, p=0.003, respectively). After adjustment the femoral neck BMD for body height, the association remained (p=0.021). There was no difference in BMD values between the reference and exercise groups during intervention. Conclusions: We suggest that the VDR gene TaqI polymorphism may be affecting bone mass through an influence on body growth. The present findings also suggest that the VDR polymorphisms do not modify the effect of regular aerobic exercise on BMD.