Polymorphisms in the vitamin D receptor (VDR) gene using ultrasound (US) bone mass and bone metabolic markers were investigated as potential genetic markers for osteoporosis in 126 premenopausal Japanese women aged 27.2 +/- 10.1 (mean +/- SD) years. The relationship between their VDR gene polymorphisms and bone states was determined. VDR genotypes were based on the absence (B) or presence (b) of the Bsm I restriction site (B polymorphism), and ATG (the M allele) and ACG (the m allele) sequences at the translation initiation site (M polymorphism). Genotype frequencies were 73.8%, bb; 24.6%, Bb; 1.6%, BB; 15.1%, MM; 51.6%, Mm and 33.3%, mm. The stiffness index of calcaneal bone minerals measured by an US bone densitometer was significantly higher in the mm types (P <0.05 versus MM) than in the Mm types (P <0.01 versus MM) and MM types. There was no significant difference between in B polymorphisms. Furthermore, bone mass was correlated with serum bone type alkaline phosphatase (ALP) activity and urinary deoxypyridinoline concentration in M polymorphisms. Because the distribution of B polymorphisms in each M polymorphism genotype did not differ, M polymorphisms were affected independently from B polymorphisms to bone mass or bone metabolic markers. No significant difference was observed in nutritional intake and food consumption among genotypes. In the MM and Mm types, the bone mass was closely related to the frequency of milk intake during the periods of elementary and junior high school. In contrast, bone mass was not associated with nutritional intake or the frequency of past milk intake in B polymorphisms. Therefore, the M polymorphism of the VDR gene is a stronger genetic indicator of osteoporosis than the B polymorphism in premenopausal Japanese woman.