For the first time, an analysis of five Alu insertion loci (ACE, APOA1, B65, PV92, TPA25) has been carried out in 10 Russian populations (1088 individuals) covering the whole historical area of the Russian ethnos. Depending on the locus, Russian populations exhibit similarity to their Western (European populations) or Eastern (populations of the Ural region) neighbors. Considering the frequencies of the studied Alu-insertions, the Russian gene pool exhibits low variation: average interpopulation variation (d) was 0.007, whereas on classical markers, mtDNA and Y chromosome, heterogeneity of the Russian gene pool is essentially higher (0.013, 0.033, 0.142, respectively). Therefore, on the intra-ethnic level, this set of five Alu insertions has low variation. However, a clear pattern was obtained in inter-ethnic comparison of 13 East European ethnic groups, which formed three clusters in accordance with their historical and geographical position: East Slavic, Caucasian and South Ural clusters. The obtained data confirm the efficiency of using Alu insertions for studying genetic differentiation and gene pool history of East European populations.