Osteoporosis and obesity are important public health problems in an aging society. We investigated the differential impacts of fat on bone mineral density (BMD) according to gender and menopausal status. We analyzed the baseline data of an ongoing observational cohort study, including a total of 502 healthy subjects 20-88 years of age (144 men, 159 premenopausal women, 199 postmenopausal women). Body composition and fat mass were measured using computed tomography and dual energy X-ray absorptiometry (DXA). BMD was measured at lumbar spines using DXA. In men and postmenopausal women, there was no significant correlation between fat and bone parameters after adjusting for age and body weight. However, in premenopausal women, BMD had significant negative correlations with waist circumference, total fat area, subcutaneous fat area, appendicular fat mass and percentage fat mass after adjusting for age and body weight. Furthermore, only in premenopausal women, the subjects with the highest quartile of percentage fat mass had the lowest BMD even after adjusting for confounding factors including age, body weight, physical activity, alcohol use and smoking history. Multiple linear regression analysis showed that percentage fat mass was a significant negative decisive factor for BMD in premenopausal women. Our study showed the differential relationship between fat mass and BMD according to gender and menopausal status. Only in premenopausal women did fat mass have a significant negative effect on bone mass. This result suggests the importance of reducing fat mass in order to achieve peak bone mass in young adult women.