Heavy alcohol drinking is an important risk factor for some lifestyle-related diseases. However, the relationship between drinking habits and medical care expenditures has not been elucidated in a Japanese general population. We examined this relationship in a 9-year cohort study. Study participants were 2039 National Health Insurance beneficiaries aged 40-69 years living in a rural Japanese community. The baseline survey, with medical check-up, was performed in 1989 or 1990 and the subjects' drinking habits were estimated by questionnaire. Medical care use and costs were monitored by linkage with the National Health Insurance claim history files at baseline survey through the end of March 2000. Men who were daily heavy drinkers (ethanol intake > or =69 g per day) had significantly higher medical costs compared to participants who drank less, within 5 years after baseline. This difference was 2000 yen per month after adjusting for age, body mass index, smoking, systolic blood pressure, glycosuria, serum total cholesterol and alanine aminotransferase. Daily heavy male drinkers also had a higher hazard ratio for total mortality compared to occasional drinkers, by the Cox proportional hazard model (hazard ratio: 1.81), although it did not reach statistical significance (P = 0.153). In women, medical costs were almost the same for occasional and daily drinkers. Total medical costs among Japanese men aged 20 years and over may be decreased by about 8400 billon yen per year if we assume a 20% decrease in daily heavy drinkers. To reduce national medical costs, it is important to promote a program for heavy drinkers, as described in the "Health Japan 21" initiative, the Japanese national health promotion guidelines for the first 10 years of the 21st century.