A method utilizing hydrogel biological microchips was developed to genotype markers of human Y-chromosome haplogroups. With the method, 14 core haplogroups and their 78 subclades were determined, including (subclade markers are in parentheses) B-M60, C-M130 (F1906, Z18160, F6370, Y4630, Z4063, and M407), D-CTS3946, E-M5388 (P177, M5017, L539, L618, L677, Z827, M123, L29, and L791), G-P257 (F858, P15, Z6552, and L1259), H-M2920, I-U179 (M253, Z2336, Z58, M438, S2648, M436, and L596), J-M304 (PF4641, Z2363, CTS3569, CTS886, M410, PF5125, PF5130, Z7671, Z2221, and Z2417), L-M185 (Z5919, Y6288, and PH3615), N-M231 (L395, CTS10075, CTS10760, and CTS10082), O-M175 (M1422, F36, and M134), Q-M1105 (L472, L74, YP344, M7361, and L275), R-P224 (M420, S224, Z283, Z2906, CTS11962, Z91, Z686, S3357, YP237, Y33, Z93, L657, Z2124, Z2125, Z2123, Y20746, Y934, S23592, Z2122, M343, M73, CTS894, M412, M405, P312, Z2103, and M479), and T-M272. Genotyping included multiplex PCR followed by hybridization on a biochip. Haplogroup frequencies were determined in a sample of 356 males living in European Russia. The direct method can provide an alternative to indirect determination of haplogroups by Y-STR haplotype with the use of predictors. The method was developed with due regard to requirements for forensic genotyping methods and was primarily designed to obtain forensic information on the biogeographical origin of the person in question. The average amplicon length was 72 bp. The study clarified the population structure of Y haplogroups in the Slavic population of European Russia.