An inverse association between blood cholesterol level and excess mortality in low cholesterol level subjects has been reported, but there has been no reasonable explanation widely accepted. To evaluate the associations between unfavorable factors and low blood cholesterol in non-Western populations, we performed a cross-sectional study in a rural Japanese population. A self-administered questionnaire concerning health characteristics and a nutritional survey, using a continuous 48-hour dietary record, was conducted on 461 males and 571 females aged 20-79 years old. The serum total cholesterol (TC) of less than 160 mg/dl was defined as low cholesterol, which accounted for 18% of the subjects. The multivariate odds ratio of having low cholesterol adjusted for age and selected variables were 0.70 (95% Cl: 0.52-0.94) for 1 SD increment of Key's lipid factor, 0.71 (0.51-0.97) for 1SD increment of vitamin A intake, 2.23 (1.01-4.91) for heavy drinking, 2.80 (1.21-6.46) for being underweight and 2.59 (1.01-6.61) for blood transfusion in males, and 1.04 (1.00-1.08) for 10 cigarette-year increase in smoking in females. Even when further adjusted for body mass index, these associations were still significant except for those who were underweight and had undergone blood transfusion in males. These findings may partly explain the excess mortality of the Japanese males with low serum TC.