A biochip has been developed that enables one to determine Y-chromosome haplogroups C, DE, G, H, I, J, L, N, O, and R in the DNA sample. SNPs M130, M145, P257, M69, U179, M304, M185, M231, M175, P224 were selected as haplogroup markers, correspondingly. The genotyping included two-round PCR with fluorescent labeling of the product followed by hybridization with immobilized probes on the biochip. An analysis of the ratios of fluorescent signals for immobilized wild-type probe-group specific probe pairs for each of the chosen polymorphic markers showed a high accuracy Y-haplogroup genotyping using the biochip. The reliability of genotyping was confirmed by direct sequencing.