BACKGROUND We investigated the association between body composition, especially truncal or non-truncal fat mass (FM), and bone mineral density (BMD) in premenopausal women in Korea. METHODS A cross-sectional study was performed using data from the Korea National Health and Nutrition Examination Survey IV and V (2008-2011). Total lean mass (LM), total FM (TFM), truncal FM, and non-truncal FM, and BMD of the total femur, femoral neck (FN), and lumbar spine were measured using dual-energy X-ray absorptiometry. The association between body composition and BMD was analyzed using multiple linear regression. The risk of low BMD according to quartiles of TFM, truncal FM, and non-truncal FM was calculated using logistic regression. Subgroup analysis according to body mass index was also performed. RESULTS In 4,343 premenopausal women, total LM was positively associated with BMD regardless of weight adjustment. TFM, truncal FM, and non-truncal FM were inversely associated with BMD after adjusting for weight. Odds ratios (ORs) for low BMD and 95% confidence intervals (CIs) of the highest quartile of TFM, truncal FM, and non-truncal FM compared with the lowest quartile were calculated. The risk of low BMD of the FN was higher in the highest quartile of TFM (OR, 4.48; 95% CI, 1.11-18.01) and truncal FM (OR, 5.48; 95% CI, 1.75-17.20). Truncal FM and not-truncal FM had an inverse association with BMD in the non-obese and obese subgroups of women. CONCLUSIONS Total LM has a protective effect on BMD and FM can have a detrimental effect on BMD besides its skeletal loading effect.