Recent studies have suggested that natural agents such as isoflavones, resveratrol, and anthocyanin have beneficial effects on metabolic syndrome-related disorders. The objective of this study was to evaluate dietary isoflavone intake, urinary isoflavone level, and their relationship with the risk of metabolic syndrome (MetS) among Korean postmenopausal women. The subjects included 46 MetS and 60 controls. The MetS risk score was determined by adding the number of risk factors such as waist circumference, blood pressure (BP) and levels of triglyceride (TG), HDL-cholesterol, and glucose. Dietary isoflavone intake was not significantly different between the MetS and control groups; however, the urinary daidzein level was significantly higher in the MetS subjects compared to that of the controls. Subjects with high TG had higher urinary daidzein and isoflavone (daidzein + genistein) levels than those without such abnormalities. But, the MetS risk score showed no significant correlation with urinary daidzein, genistein, and isoflavone excretions.