The relationship of bone mineral density (BMD) and bone metabolic markers in women is an interesting field of research. In this study, we aimed to clarify the relationship of body weight, bone metabolic markers and BMD. The subjects were 72 women. The levels of serum bone-specific alkaline phosphatase (BAP), serum type I collagen-cross-linked peptide (s-NTx) and urinary deoxypyridinoline (u-DPD) were measured. The associations between dependent variables (BMD changes/1 or 4 years in the lumbar spine and femoral neck) and explanatory variables (body weight changes/1 or 4 years, the levels of BAP, s-NTx, u-DPD) were evaluated using multiple regression analysis. Changes in the lumbar spine BMD were significantly correlated with changes in height over a year, and those of the femoral neck were significantly correlated with changes in weight over a year. Changes in the lumbar spine BMD over 4 years were significantly correlated with age, BAP and the changes of weight over 4 years. Changes in the femoral neck BMD over 4 years were significantly correlated with the changes in weight for 4 years. These results suggest that BMD changes of different bones correlate with different explanatory variables and that, to predict BMD changes from bone metabolic markers in women, it is necessary to measure BAP levels.