A genotyping method of biological material for ABO, HLA-DQA1 and AMEL loci is described. The method is based on allele-specific SNP determination using the hydrogel biochips technology. The amplified fluorescently labeled fragments of the genes were hybridized with specific DNA probes immobilized on a biochip. The allele/genotype assignment was done according to the distribution of fluorescent signal. The minimal amount of biological material is corresponded to 100 pg of DNA. The method was proved using control samples with known genotype. Using biochips 442 DNA samples belonging to the East Slavic population group were genotyped. The allele frequencies of ABO and HLA-DQA1 loci were determined. The possibility of genotyping of biological traces, including the stubs of filter cigarettes, material from the lip of the glass was demonstrated. This method can be used for genetic testing in forensic studies. The probability that the determined genotype belongs to a concrete individual was estimated as 99.6%.