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We investigated the independent associations of total and beverage-specific ethanol consumption with body mass index (BMI) and waist-to-hip ratio (WHR) in middle-aged Japanese males, because of the scarcity of epidemiologic data in Japan. The subjects were 2227 male self-defense officials who received a pre-retirement health examination at the Self-Defense Forces Fukuoka, Kumamoto, and Sapporo Hospitals. Data on alcohol intake, smoking, physical activity, and past medical history were obtained from a self-reported questionnaire. Height, weight, and waist and hip girth measurements were obtained at the examination. Multiple linear regression analysis was employed. Alcohol intake was positively and strongly associated with WHR (p = 0.0001), but not associated with BMI after adjustment for lifestyle variables, including either BMI or WHR. Subjects who consumed 15 ml per day or more of shochu ethanol showed a larger WHR than never drinkers, and a dose-response relationship was found. Dose-response relationships to other beverages were not found. Dose-response relationships to other beverages were not found. These findings suggest that alcohol intake is strongly and independently associated with WHR, but not with BMI. Abdominal obesity was positively associated with shochu ethanol, but not with other types of alcohol.