A possible protective effect of coffee or caffeine intake in the formation of gallstones has been suggested in some epidemiological studies. We examined the relation of coffee, green tea, and caffeine intake to gallstone disease in middle-aged Japanese men, distinguishing known gallstones from unknown diagnosed gallstones. Study subjects were 174 cases of gallstones as determined by ultrasonography, 104 cases of postcholecystectomy, and 6889 controls of normal gallbladder in the total of 7637 men who received a health examination at four hospitals of the Self-Defense Forces (SDF). Of the 174 cases of prevalent gallstones, 50 had been aware of having gallstones. Previously diagnosed gallstones and postcholecystectomy were combined as known gallstone disease. The consumption of coffee and green tea was ascertained by a self-administered questionnaire, and caffeine intake was estimated. Statistical adjustment was done for body mass index, smoking, alcohol use, rank in the SDF, and hospital. Coffee and caffeine intake were associated each with a statistically significant increase in the prevalence odds of known gallstone disease, but unrelated to newly diagnosed gallstones. Adjusted odds ratios of known gallstone disease were 1.7 (95% confidence interval [CI] 1.1-2.8) for coffee consumption of five cups or more per day vs. no consumption and 2.2 (95% CI: 1.3-3.7) for caffeine intake of 300 mg/day or more vs. less than 100 mg/day. The consumption of green-tea showed no material association with either unknown gallstones or known gallstone disease. The findings do not support a hypothesis that coffee drinking may be protective against gallstone formation.