Allele frequencies of two Y chromosome-specific short tandem repeats, locus DYS385 and DYS19, in addition to the Y Alu polymorphic (YAP) insert (DYS287) were investigated in blood samples obtained from 270 unrelated Japanese in Miyazaki Prefecture (south Japan). A total of 47 genotypes in DYS385 and 6 in DYS19 were detected, and the frequency of the YAP+ allele was found to be 35.2% (95/270). The allele distributions of each locus revealed significant differences compared with those in other populations. One hundred and twelve different haplotypes were observed in the combined 55 alleles of three loci. The gene diversity values range 0.96 for DYS385 and 0.71 for DYS19, and the combination haplotype diversity value is 0.98.