As one approach to exploring whether the mitochondrial DNA 5178 adenine/cytosine (mt5178 A/C) polymorphism is associated with atherosclerosis, we genotyped 461 healthy Japanese individuals and studied the relationship of mt5178 A/C genotypes to serum lipid levels. Blood specimens were obtained after at least a 12-h fasting period from the subjects. The mt5178 A/C was genotyped by the polymerase chain reaction/restriction fragment length polymorphism method. The relative frequency of mt5178 A was 41.6% (192/461) and of mt5178 C was 58.4% (269/461). After adjustments for age and body mass index, the high-density lipoprotein cholesterol concentration in males carrying mt5178 A was significantly higher than that in males carrying mt5178 C ( P=0.026). The tryglyceride (TG) concentration in females carrying mt5178 A was significantly lower than that in females carrying mt5178 C ( P=0.012). This difference in the TG level between the two genotypes was more evident in postmenopausal females than in premenopausal females. Mt5178 A seems to have an antiatherogenic effect. This is the first genetic epidemiological report on the association of mt5178 A/C polymorphism with serum lipid levels in the Japanese population.