In Japan, metabolic syndrome used to be rare, and the level of coffee consumption was low. However, the Japanese life style has been changing rapidly, and these changes have been associated with a steady increase in the frequency of metabolic syndrome and with greater consumption of coffee. We examined the relationship between metabolic syndrome and the consumption of coffee or green tea. A total of 1902 Japanese aged over 40 years (785 men and 1117 women) received population-based health check-up in 1999. We measured components of metabolic syndrome (blood pressure, waist circumference, fasting plasma glucose, and lipid profiles). Eating and drinking patterns were evaluated by a food frequency questionnaire. Multivariate analyses were performed to clarify the association between coffee or green tea consumption and the components of metabolic syndrome. All components of metabolic syndrome except for HDL-cholesterol were significantly (p<0.01) and inversely related to coffee but not green tea consumption by multivariate analysis after adjusting for confounding factors. The larger was the number of components of metabolic syndrome, the lower was the level of coffee consumption (p<0.0001). In addition, there was a high frequency of metabolic syndrome in small coffee drinkers. Thus, coffee but not green tea consumption was inversely associated with metabolic syndrome.