The mitochondrial DNA HV3 region contains CA dinucleotide repeats which display length polymorphism. To analyze this for forensic purposes, we designed a fluorescence-labelled PCR primer set for short amplification products and carried out genotyping by using capillary electrophoresis. A total of 4 alleles with 4-7 repeat units were observed and the genetic diversity was estimated to be 0.5120 in 500 unrelated Koreans. Interestingly, three individuals showed two or three length variants, i.e. length heteroplasmy.