Cross-sectional associations between lifestyle factors [cigarette smoking, alcohol intake, overall obesity indicated by body mass index (BMI), eating breakfast, snacking between meals, considering nutritional balance, coffee drinking, physical exercise, and hours of work and sleep] and serum lipid and lipoprotein levels were examined in 1580 middle-aged Japanese men in Osaka, Japan. From stepwise regression analyses, significant correlates with low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and Log triglyceride levels were, in the order of relative importance: BMI, alcohol intake (negative), and age for LDL cholesterol level; BMI (negative), cigarette smoking (negative), alcohol intake, considering nutritional balance, and physical exercise for HDL cholesterol level; and BMI, cigarette smoking, working hours (negative), considering nutritional balance (negative), alcohol intake, and coffee drinking (negative) for Log triglyceride level. The cumulative percentages of variation for LDL cholesterol, HDL cholesterol and Log triglyceride levels were 4.2%, 15.4% and 14.7%, respectively. From stepwise regression analyses, excluding BMI as a factor in the model, snacking between meals emerged as a significant factor for LDL cholesterol level and HDL cholesterol level (negative). The cumulative percentage of variation for each serum lipid and lipoprotein level was decreased (1.5% for LDL cholesterol, 6.8% for HDL cholesterol, and 3.1% for Log triglyceride). These results suggest that BMI has the strongest association with serum lipid and lipoprotein levels and that good daily lifestyles may have an anti-atherogenic effect by altering serum lipid and lipoprotein levels in middle-aged Japanese men.