Introduction. Genetic susceptibility to Type 2 Diabetes (T2D) with a complex mode of inheritance is explained by the presence of multiple gene, each conferring a small moderate contribution the overall risk, as well as by alternative combinations of genes. Due to the success of Genome—Wide Association Study there has been rapid increase in the availability of genetic data for T2D. This allows the collection of large sets of genetic polymorphic loci, which could be key in the understanding of the genetic basis of T2D. The aim of this study was to determine alleles and allelic combinations that are associated with T2D phenotype. Material and methods. We assessed the associations of 96 single nucleotide polymorphisms (SNPs) linked with T2D different pathway components and carbohydrate metabolism abnormalities in 96 Russian patients and 96 normoglycemic controls using Illumina Golden Gate Genotyping Assay (low density DNA chip with 96 SNPs). T2D was defined according to the World Health Organization criteria, 1999. Data were analyzed with the free online statistical program named “Calculator for confidence intervals of odds ratio” (www.gen-exp.ru/calculator_or.php) and APSampler software (https://code.google.com/p/apsampler) for multi-locus association analysis. Results. On the first stage of the study we detected ten SNPs that can be independently contributing to T2D risk in the Russian cohort, they are rs8050136 (p=0.05) and rs11642841 (p=0.04) in FTO gene, rs2943641 (p=0,02) and rs2943634 (p=0.03) in IRS1 gene, rs571312 in MC4R gene, rs1470579 (p=0.04) in IGF2BP2 gene, rs163184 (p=0.03) in KCNQ1 gene, rs11924032 (p=0.04) in SLC2A2 gene, rs11634397 (p=0.03) in ZFAND6 gene, rs7172432 (p=0.04) in C2CD4A gene. On the second stage we found a biallelic combination of A allele rs8050136 in FTO gene and A allele rs7172432 in C2CD4R gene that was associated with T2D risk. Remarkable, the combined effect (association) of rs8050136 and rs7172432 was stronger (OR=1,97; p=0.006) than that of each SNP alone. Conclusion. The biallelic combination of A allele rs8050136 in FTO gene and A allele rs7172432 in C2CD4R gene can be used as a genetic marker of T2D.