This study was conducted to investigate the association between the metabolic syndrome (MS), which includes a cluster of major risk factors for cardiovascular diseases, and bone mineral density (BMD) from a population-based study. This cross-sectional study was based on a nationwide representative survey data from the Korean National Health and Nutrition Examination Survey (KNHANES) 2008. A total of 3,207 subjects were included from the KNHANES 2008 and composed of men (mean age 48.4 years), premenopausal women (mean age 36.5 years) and postmenopausal women (mean age 64.8 years). The MS was identified according to the new criteria from a joint scientific statement endorsed by major organizations including the National Heart, Lung, and Blood Institute. The mean age of study participants was significantly different according to MS status (58.2 years in the MS group vs. 45.7 years in the non-MS group, P < 0.001). The association between MS and BMD at the lumbar spine and proximal femur was analyzed with adjustment for potential confounders. Although the adjusted BMD at all skeletal sites was not significantly different between participants with and without MS, an increased number of MS components was associated with low adjusted femoral neck (FN) BMD only in men (P = 0.01). After adjusting confounding factors, the triglyceride component of MS was related to low FN BMD in men, but to high BMD at all of the skeletal sites measured in postmenopausal women. The glucose component of MS showed an association with high adjusted BMD at total hip in men. Men with MS had significantly higher odds for pooled osteopenia and osteoporosis (odds ratio: 1.49, 95 % confidence interval: 1.04-2.14). In conclusion, low BMD is associated with MS in Korean men, and the association between the MS component and the BMD is different according to gender.