An analysis of eight Alu insertion loci (ACE, ApoA1, PV92, TPA25, NBC27, NBC102, NBC148 and NBC182) was carried out in three ethnic groups of the South Caucasus (Abkhazians, Armenians and Georgians). Genetic differentiation between these groups (Gst = 1%) was half as much as in European populations and four time less than in populations of Dagestan. Although it was not possible to determine a contribution of Neolithic farmers to the Caucasian gene pool, the principal component analysis showed clear differences between these populations and those of Europe, Siberia and Asia. No evidence of correlation between genetic and linguistic data in our populations was disclosed. However, long-term habitation on common territory has led to common cultural, anthropological and detectable genetic traits.