Objective: Individual population history is the main reason for the variability of linkage disequilibrium (LD) patterns and haplotype frequencies among populations. Such diversity may influence the transferability of tag SNPs from one population to another. Our goal was to compare patterns of pairwise LD and allele and haplotype frequencies in Estonian and Russian populations, to estimate the genetic variation between populations and assess the potential transferability of tag SNPs. Methods: 452 SNPs from 25 unlinked genomic regions on 12 chromosomes were genotyped in 140 Estonians and 207 Russians from Northern and Western regions of the European area of Russia. Results: The allele frequency distributions were highly consistent between populations (R > 0.90 for all pairwise comparisons). The overall frequency variation among populations was low (FST = 0.0054). The number of SNPs with high-range FST values (0.02–0.09) was most prominent for the MC5R genomic region. Haplotype heterogeneity among populations was low (FST values ranged within 0.00–0.01, with the exception of haploblocks in the ADIPOR2 and MC5R regions). The interpopulation proximity was also evaluated using haplotype diversity. Conclusion: Our data showed a high concordance between the populations studied, which may be considered as the result of their historical formation on a cognate genetic basis.