BACKGROUND: Increased body fat was associated with insulin resistance, glucose and lipid metabolism, and blood pressure and non-exercise is risk factor for metabolic syndrome. But, the studies considering both body fat and exercise were lacking in Korea. We, therefore, studied relationship between exercise, body fat and metabolic syndrome among Korean. METHODS: In this study, the subjects included 9,234 (Male; 5,358 Female; 3,876) who had visited one health promotion center from March, 2007 to February, 2008 and their age range is 20~79 years. Following an overnight fasting, blood samples taken from antecubital vein were used for the determination of the blood TG (Triglyceride), HDL (High density lipoprotein), LDL (Low density lipoprotein). Body mass index (kg/m2), body fat percentage, and waist circumference were measured as obesity indices. RESULTS: Over body fat (Male > or = 20%, Female > or = 30%) was independently risk factor for metabolic syndrome, from 30th to 60th, and both over body fat and non-exercise were independently risk factor for metabolic syndrome in 50th (Male; non-exercise, OR = 1.397, P = 0.039, over body fat, OR = 7.215, P < 0.001; Female; non-exercise, OR = 1.831, P = 0.002, over body fat, OR = 3.529, P < 0.001). As based on normal body fat group with doing exercise, over body fat group with not doing exercise, over body fat group with doing exercise and normal body fat group with not doing exercise were showed the increase of metabolic syndrome in 50th, respectively, OR = 8.304, P < 0.001; OR = 5.624, P < 0.001; OR = 0.875, P = 0.791 in male, OR = 8.127, P < 0.001; OR = 4.894, P < 0.001; OR = 2.739, P = 0.030 in female. In pearson chi-square, exercise was showed to decrease 27% of body fat percentage in male (P = 0.019) and 28% of that in female (P = 0.019). CONCLUSION: Body fat was more contributed to metabolic syndrome than exercise.