Background: Although an association between benign digestive diseases and smoking or drinking habits was reported, consistent results have not been obtained either in European, American or Japanese populations. Methods: Smoking and alcohol habits as risk factors for the incidence of gastric ulcer, duodenal ulcer, chronic liver disease and cirrhosis as well as cholelithiasis were examined using the longitudinal data of the Adult Health Study collected biennially between 1958 and 1998. During 1958–1998, 1,093 gastric ulcers, 437 duodenal ulcers, 2,054 chronic liver diseases and cirrhoses, and 1,136 cholelithiasis cases were newly detected based on medical history, fluoroscopy or endoscopy and ultrasonography. Smoking and drinking histories were obtained from five and three questionnaires, respectively, administered during different periods. The relative risks (RRs) for ever smoked to never smoked and that for ever drank to never drank were estimated after adjustment for city, sex, age, birth cohort, calendar time and radiation dose. Results: The analysis showed a positive association of smoking with gastric ulcer (RR: 2.03, 95% CI: 1.71–2.41), duodenal ulcer (RR: 1.31, 95% CI: 0.99–1.72), chronic liver disease and cirrhosis (RR: 1.23, 95% CI: 1.08–1.39) and cholelithiasis (RR: 1.19, 95% CI: 1.02–1.40), and a positive association of drinking with chronic liver disease and cirrhosis (RR: 1.10, 95% CI: 0.99–1.23). Conclusions: Thepeptic ulcer, chronic liver disease and cholelithiasis incidence increased significantly with smoking, and the chronic liver disease incidence increased significantly with drinking simultaneously in a prospective study of a Japanese population.