The Karachay-Malkar population of the Northwestern Caucasus Mountains has an unclear history. Oral traditions say that they are descended from Alans, who were ancient Iranian tribes. The language they speak is a Kipchak Turkic language, and was supposedly brought to the Caucasus by the invading Qumans from the Minusinsk Basin (Yenisei River-Altai Mountains). They are also supposedly related to the Bulgars, and the name Malkar/Balkar is evidence for this affiliation. To elucidate their genetic past, this study compares the frequency of Karachay mitochondrial DNA haplogroups from 67 individuals with previously published results from other populations nearby. In general, it was hypothesized that the Karachays would be more similar to other Caucasus populations and Central Asian Turkic populations. Results indicate that the most similar population was indeed a Caucasus population, the Adygei, but other Caucasus populations and geographically close populations in the region were not similar in haplogroup frequency. Eastern Iranians were the next most similar, and indicate that the theory inolving ancestry to the Scythio-Iranians (Alans) may be true. Also, Altaians showed similar haplogroup types, and somewhat similar frequencies. They might indicate the ancient Turkic origins of the Karachays from the Altay Mountains. This study was helpful in clarifying some aspects of the Karachay past, but further research is needed in both the fields of mitochondrial DNA analysis and Y-chromosome analysis to identify paternally inherited genetic influences on the Karachay population.