We examined genetic variation in nine populations of Dagestan using 11 autosomal Alu insertion polymorphisms to investigate the genetic structure of indigenous groups and to assess their genetic relationship with world populations. Genetic differentiation among mountain inhabitants (GST=2%) is comparable to that for European populations. Traces of genetic drift are detectable only for endogamous and small Ando-Dido-speaking ethnic groups, and they coincide with the most linguistically diverse region of Dagestan. Multidimensional scaling analyses among West Eurasian populations revealed that mountain inhabitants of Dagestan are closely related to Anatolian and Cyprus Turks. Thus our frequency data are consistent with the available Y-chromosome data, according to which the Middle East and the Caucasus share a considerable portion of the gene pool. Overall, our results corroborate the initially suggested genetic contribution of Middle Eastern populations to Caucasus populations.