Abstract Five Y chromosomal short tandem repeat (STR) loci DYS389I, DYS389II, DYS439, DYS438 and DYS392 have been analysed to obtain the allele and haplotype frequencies data in 129 unrelated Japanese male individuals living in Kanagawa by means of multiplex PCR with Y-PLEX™ Primer Mix, followed by capillary electrophoresis using the ABI PRISM 310 Genetic Analyzer. The gene diversity values ranged from 0.555 (DYS439) to 0.737 (DYS389II). A total of 72 haplotypes was detected, of which 51 haplotypes were unique and the others occurred at least two times. The most common haplotype (DYS389I, DYS389II, DYS439, DYS438, DYS392) was 14–30–12–13–13 with a frequency of 10%, and the haplotype diversity was calculated as 0.969. The combined resolutions of the five Y STR multiplex system using the Y-PLEX™ 5 was applicable to routine case work.