Total bilirubin, not direct or indirect bilirubin, has been reported to associate inversely with metabolic syndrome. Therefore, we aimed to evaluate the association between bilirubin subtypes and metabolic syndrome among the Korean population. This study included 5,231 Koreans (3,008 men, 2,223 women) aged 30-87 years, who visited the Health promotion centers in Seoul from April, 2006 to June, 2007. The associations of direct, indirect, and total bilirubin classified in quartiles with metabolic syndrome were measured by logistic regression analyses in men and women. Odds ratios (95% confidence intervals) of the lowest, 2nd and 3rd quartiles of direct serum bilirubin compared with the highest quartile (reference) were 2.3 (1.6-3.2), 1.8 (1.3-2.4), and 1.8 (1.4-2.4) among men, and 5.5 (2.6-11.5), 3.1 (1.5-6.7), and 1.9 (0.9-4.3) among women, respectively. In a multivariable adjusted model, however, the significance of inverse associations with total and indirect bilirubin became attenuated. The relation was consistent particularly with direct bilirubin in subgroups of metabolic syndrome components such as central obesity, hypertriglyceridemia, hyperglycemia, and low HDL-cholesterol in both men and women. Of the three subtypes of serum bilirubin, the inverse association of metabolic syndrome was significantly apparent and consistent with direct bilirubin.