We analyzed 11 Y-STR loci (DYS446, DYS447, DYS449, DYS450, DYS459a/b, DYS463 and DYS464a/b/c/d) in a total of 324 Japanese males from western and southern Japan. Gene diversity ranged from 0.958 at DYS464 in western Japan to 0.259 at DYS450 in southern Japan. A total of 272 different haplotypes were observed, of which 240 were found in single individuals. The overall haplotype diversity and discrimination capacity was 0.9982 and 0.8395, respectively.