Fermented soybeans (Natto), a traditional Japanese food, contain more than 100 times as much vitamin K2 as various cheeses and are considered to promote gamma-carboxylation. Thus it is conceivable that Natto may play a preventive role in the development of osteoporosis. In this study, the relationships between the bone stiffness index measured by ultrasound, bone turnover markers, and lifestyle factors, including Natto intake, were examined in relation to vitamin D receptor (VDR) polymorphism. Among 117 premenopausal volunteers, approximately 75% were bb homozygotes, 20% were Bb heterozygotes, and only 5% were BB homozygotes. The B allele group and the bb group were subdivided according to Natto intake. In a monovariate analysis, no significant differences in indices for dietary intake, including Ca and vitamin D intake, were observed. The stiffness index in the B allele group, however, was slightly lower than in the bb groups when there was no Natto intake. There were no significant differences in serum ALP and Gla-osteocalcin, bone formation markers, or NTx and Ca in urine, bone resorption markers. A logistic regression test, including the interactional effect of Natto intake and VDR RFLP, indicated that the B allele group was a risk factor of bone mineral loss and that Natto was effective in maintaining bone stiffness in this group. Although the present study was cross sectional and requires longitudinal investigation, Natto may improve the bone health of people who have a low affinity receptor for vitamin D.