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Sex determination presents a difficult problem in archaeology and anthropology in cases of fragmentary or juvenile remains, and where grave goods are absent. Here, a molecular genetic analysis of the sex of human remain from the Early Medieval cemetery at Nefedievo, North Russia, was carried out and the results were compared with archaeological and anthropological data. Teeth without cavities (15 samples) and bones (9 samples) were used as the ancient DNA source. The repetitive sequences in DYZ1, DYZ3, DXZ3 loci, and a unique sequence in the first intron of the X-Y homologous gene amelogenin, were amplified. Sex was determined in 87.5% of the samples by archaeological criteria, in 95.8% of the samples by anthropological methods, and in 79.2% of the samples by DNA analysis. PCR allowed the sex of infant's remains to be identified in individual where the sex could not be determined by anthropological methods and in three remains where sex could not be inferred from archaeological data. Uneven preservation of nuclear DNA loci was evident.