Objective. Previous studies have shown that coffee consumption is inversely related to serum levels of liver enzymes such as alanine aminotransferase (ALT), aspartate aminotransferase (AST), and gamma-glutamyl transferase (GGT), but few have addressed the relation in women and effect modifications of alcohol use and obesity. We examined the association of coffee and green tea consumption with serum activities of liver enzymes in free-living Japanese men and women, focusing on sex difference and effect modifications of alcohol and obesity. Material and methods. The data were derived from the baseline survey of the Kyushu University Fukuoka Cohort Study, and included 12,020 Japanese men and women aged 49-76 years who were free of chronic liver diseases. Results. There was an inverse association between coffee consumption and elevated ALT in men, and the association between the two was weaker in women. In the analyses stratified by aminotransferases category, inverse associations of coffee consumption with serum activities of liver enzymes were observed in both men and women within the whole range and among those with aminotransferases within the reference range (ALT/AST < 40 IU/L for men and ALT/AST < 30 IU/L for women). Inverse associations of coffee with liver enzymes were more evident in those with high alcohol consumption and in those with low body mass index. Conclusions. Coffee drinking probably confers protection against alcohol-related increase in liver enzymes.