We examined sequence variations in the mitochondrial DNA (mtDNA) control region, tRNA leucine1 ( tRNA leu1) and cytochrome b ( CYTB) genes in order to investigate the characteristics of mtDNA polymorphisms and haplogroups in Korean population. Seventy maternally unrelated healthy Korean donors provided blood samples for the present study. The small deletion mutations exist only in the hypervariable region (HV) region. The Korean population exhibited a high level of length heteroplasmy in the 16184-16193 and 303-315 poly-C regions from the mtDNA control region. Some of the most common polymorphisms found in all subjects were 73A > G, 263A > G, 3107delC and 15326A > G from HV2, HV1, tRNA leu1 and CYTB genes, respectively. The most common haplogroup in the Korean population was D4 which was found in 16% of the population, followed by A, B, B4a, D5, G1a and M10 (each of 6%). Several haplogroups appear to be restricted to the Japanese and Korean populations. However, the current study revealed different distribution of some haplogroups in the Korean population in comparison with a previous study. The overall pattern and frequency of haplogroups among Koreans in the current study were closer to those of a Japanese population than to a Han Chinese population.