Japanese fermented soybeans (natto in Japanese), which contain a large amount of menaquinone-7, may help prevent the development of osteoporosis. We assessed the possibility of an association between habitual natto intake and bone mineral density (BMD) and BMD change over time in healthy Japanese women who participated in a large representative cohort study (Japanese Population-based Osteoporosis Study: JPOS study). The BMD was measured at the spine, hip, and forearm in 944 women (20-79 y old) at baseline and at a follow-up conducted 3 y later. Dietary natto intake was assessed by a FFQ on both occasions. Additional covariates including age, height, weight, lifestyle factors, dietary calcium intake, and the intake of other soybean products, were also measured. The total hip BMD at baseline increased (P for trend = 0.0034) with increasing habitual natto intake in the postmenopausal women, although this was not the case at other skeletal sites. There were significant positive associations between natto intake and the rates of changes in BMD at the femoral neck (P < 0.0001) and at the distal third of the radius (P = 0.0002) in the postmenopausal women. The association in the femoral neck persisted even after adjusting for covariates. No significant association was observed between the intake of tofu or other soybean products and the rate of BMD change in the postmenopausal women. Natto intake may help prevent postmenopausal bone loss through the effects of menaquinone 7 or bioavailable isoflavones, which are more abundant in natto than in other soybean products.