Two microsatellite markers, D16S283 and D16S284, closely linked to the locus of autosomal polycystic kidney disease (PKD1), were amplified in a Japanese population sample by the polymerase chain reaction to investigate differences in allele frequencies between Japanese and Caucasian populations. Ten D16S283 alleles and four D16S284 alleles were discerned among 53 Japanese. The observed heterozygosities of D16S283 and D16S284 in this study were 76.8 and 9.1%, and the polymorphism-informative contents were 0.75 and 0.09, respectively. Several allele frequencies of D16S283 exhibited significant differences. The Y9 allele (19 CA repeats, 91 bp) was the most frequent in both populations but its frequency in Caucasians was higher. The second most frequent allele was different: Y6 (22 CA repeats, 97 bp) in Japanese and Y10 (18 CA repeats, 89 bp) in Caucasians. Y8 (20 CA repeats, 93 bp) and Y11 (17 CA repeats, 87 bp) alleles also showed different frequencies. For D16S284, no differences in allele frequencies were observed between the two populations. As we observed differences in allele frequencies for D16S283, an association study with this polymorphism should carefully control for the ethnic origin of subjects.