Diet and food intake play an important role in the development of osteoporosis. However, apart from calcium and vitamin D, how nutrients affect bone status is not fully understood. The purpose of this study was to determine cross-sectional and longitudinal associations between dietary intake and bone mineral density (BMD) in Japanese postmenopausal women. This 5-year cohort study included 600 community dwelling women aged 55-74 years at baseline in 2005. Information on demographics, nutrition, and lifestyle was obtained through interviews, and nutritional and dietary intake was assessed using a validated food frequency questionnaire. BMD measurements were performed by dual energy X-ray absorptiometry. In 2010, 498 women underwent follow-up BMD examinations. Multiple linear regression analysis was performed to determine associations of predictor variables with BMD, adjusting for confounders. In cross-sectional analyses, coffee or black tea consumption was positively associated with lumbar spine (P = 0.004) and total hip (P = 0.003) BMD, and alcohol intake was positively associated with femoral neck (P = 0.005) and total hip (P = 0.001) BMD. In longitudinal analyses, vitamin K (P = 0.028) and natto (fermented soybeans) (P = 0.023) were positively associated with lumbar spine BMD, and meat or meat product consumption was inversely associated with total hip (P = 0.047) BMD. In conclusion, dietary factors other than calcium and vitamin D intake are predictors of bone mass and bone loss in Japanese postmenopausal women. In particular, natto intake is recommended for preventing postmenopausal bone loss on the basis of current evidence.