To examine whether a racial difference in apolipoprotein B (Apo B) gene polymorphism between Japanese and American Caucasians corresponds with the lower blood cholesterol concentrations in Japanese than in Americans, we examined the EcoRI polymorphism of the Apo B gene for 271 nonsmoking men and women aged 47-69 years in two population-based samples: rural Japanese living in Akita and Caucasians living in Minneapolis-St. Paul, Minnesota, USA. Mean values of serum cholesterol concentrations were significantly lower in Japanese than in Caucasians for both men and women (difference = 25-26 mg/dl). An allele-specific polymerase chain reaction was conducted to examine the Eco RI cutting site at the 12669 cDNA position of the Apo B gene. The allele R2 (absence of the cutting site) has been associated with lower cholesterol concentrations in two previous studies. The frequency of the R2 allele was 6% for Japanese and 17% for Caucasians (P < 0.001), and this race difference in allele frequency was identical for men and women. After controlling for age, body mass index, alcohol intake, and for women, menopausal status and hormone replacement therapy, the adjusted mean (SE) cholesterol level among Japanese was 204 (3) mg/dl for genotype R1R1 and 185 (7) mg/dl for genotype R1R2 or R2R2 combined (P = 0.01). The respective mean values among Caucasians were 224(5) mg/dl and 232(7) mg/dl (P = 0.36). The polymorphism had a similar effect on total cholesterol concentrations for both men and women. The observed lower prevalence of the R2 allele in Japanese than in Caucasians indicates that this variation in the Apo B gene does not explain the racial difference in blood cholesterol concentrations.