The purpose of this study is to investigate the relationship between sex hormones and metabolic syndrome independent of age and BMI in Korean men.We conducted a cross-sectional study with data from a health promotion center during the period from March 2007 to February 2010. 2172 Korean men aged 21–79 were enrolled. Total testosterone, sex hormone-binding globulin (SHBG), high density lipoprotein (HDL) cholesterol, triglyceride (TG), and glucose were assessed with overnight fasting serum samples.Sex hormones were divided into quartiles; odds ratios for metabolic syndrome and each component were analyzed.Total testosterone showed negative associations with waist circumference (WC), fasting glucose, TG, blood pressure and body mass index (BMI), and a positive relationship with HDL cholesterol (P for trend <0.001, respectively). SHBG was negatively associated with WC, fasting glucose, TG, and BMI, and positively associated with total testosterone and age. Comparing with the highest quartile, odds ratios of lowest quartile of total testosterone and SHBG for metabolic syndrome were 3.01 (95% CI, 2.11–4.28) and 6.34 (95% CI, 2.29–17.58), respectively, after adjusting for age, smoking status, alcohol intake, exercise, and BMI. Total testosterone was significantly associated with each metabolic component and SHBG was associated with glucose and TG after adjustment for age, smoking status, alcohol intake, and BMI. Calculated free testosterone had no significant relationship with metabolic syndrome or its components.Total testosterone and SHBG are negatively associated with prevalence of metabolic syndrome independent of age and BMI in Korean men.