The objective of the study was to investigate the relationship between visceral and subcutaneous adiposity measured by computed tomography and bone mineral density (BMD) and to identify the metabolic factors associated with BMD. We studied 461 subjects recruited from the health-care center at Severance Hospital, Yonsei University College of Medicine. Multivariate regression analyses were conducted to examine the cross-sectional associations between body composition-related or metabolic parameters and BMD. After adjusting for body weight and other confounders, visceral fat area had an inverse association with BMD in men (beta = -0.133, P = 0.049 for lumbar spine; beta = -0.135, P = 0.037 for femoral neck; beta = -0.179, P = 0.005 for total hip) and women (beta = -0.424, P < 0.001 for lumbar spine; beta = -0.302, P = 0.005 for femoral neck; beta = -0.274, P = 0.014 for total hip). However, the subcutaneous fat area showed no statistically significant relationship with BMD at most sites. Among the metabolic parameters, HDL cholesterol was positively associated with BMD, while LDL cholesterol was negatively associated with BMD in men. In women, total and LDL cholesterol were negatively associated with BMD at the lumbar spine. We conclude that visceral adiposity is inversely associated with BMD after adjusting for confounders and that metabolic factors may partly contribute to this inverse relation.