SummaryApolipoprotein (apo) CIII Sst-I genotypes and apo AI Msp-I genotypes were investigated in 82 unrelated healthy Japanese, using genomic hybridization analysis with a 2.2 kb fragment of the human apo AI gene. The frequencies of the $2 and M2 alleles were 0.34 and 0.40, respectively, and much higher than those in Caucasians. The alleles identified by the apo CIII Sst-I and apo AI Msp-I polymorphisms were observed to be in linkage disequilibrium (A=0.206+0.012, p<0.001). Three of the four possible haplotypes were identified: the frequencies of the haplotype were S1-M1=0.604, $2-M2=0.341, and S1-M2=0.055. The data indicate that Japanese are characterized by the common presence of the haplotype $2-M2 as compared with Caucasians and that the haplotypes identified by the apo CIII Sst-I and apo AI Msp-I polymorphisms are useful genetic markers for Japanese.