Allele frequencies and haplotypes of 16 Y chromosomal STR loci included in the AmpFlSTR((R)) Yfilertrade mark system were obtained from a sample of 526 unrelated Korean male individuals. A total of 478 haplotypes were observed in the 526 individuals studied, of which 440 were unique. The overall haplotype diversity for the 16 Y-STR loci was 0.9996, and the discrimination capacity was 0.9087. We found 13 atypical alleles, including null, duplicated and microvariant alleles. Microvariants have been characterized by sequencing, 14.1 allele at DYS458 showing the flanking site mutation, 13.1 and 15.2 allele at DYS385a/b showing changes in the repeat structure.