Traces of Paleolithic exodus routes of modern humans from Africa to Europe have been studied genetically using female specific ancestral lineages via mitochondrial DNA (mtDNA). We suggest modern humans entered Europe near the Carpathian Mountains and Hungarian Valley. If so, isolated populations of highlanders in Carpathian Europe may carry a genetic fingerprint of the ancient European predecessors and illustrate the migration routes of modern humans into Europe. Lineage-specific polymorphic sites on mtDNA were analyzed in the Carpathian Highlander population. The Carpathian Highlanders genetically resemble modern Europeans when analyzed by a hierarchical haplotyping scheme; however more studies need to be undertaken to fully understand the Carpathian Highlander’s relation to the modern European population. Further analysis of European-specific subhaplogroups in Carpathian Highlanders will further clarify the relationship between this group and the rest of European inhabitants.