Principal component analysis of Y-chromosomal haplogroup frequencies among the three ethnic groups in Bosnia and Herzegovina, Serbs, Croats, and Bosniaks, showed that Bosnian Serbs and Bosniaks are by Y-DNA closer to each other than either of them is to Bosnian Croats. Genetically, on the maternal X chromosome line, a majority (>75%) of Bosnians belong to three of the eleven major European mtDNA haplogroups - H (47.92%), U (19.44%) and J (6.94%), while a large minority (>25) belongs to other rare mitochondrial lineages. The mtDNA studies shows that the Bosnian population partly share similarities with other Southern European populations (especially with mtDNA haplogroups such as pre-HV (today known as mtDNA haplogroup R0), HV2 and U1), but are for the mostly featured by a huge combination of mtDNA subclusters that indicates a consanguinity with Central and Eastern Europeans, such as modern German, West Slavic, East Slavic and Finno-Ugric populations. There is especially the observed similarity between Bosnian, Russian and Finnish samples (with mtDNA subclusters such as U5b1, Z, H-16354, H-16263, U5b-16192-16311 and U5a-16114A). The huge differentiation between Bosnian and Slovene samples of mtDNA subclusters that are also observed in Central and Eastern Europe, may suggests a broader genetic heterogeneity among the Slavs that settled the Western Balkans during the early Middle ages.