In the Czech Republic, dairy sheep have traditionally been used as a dual-purpose species, generating income from both milk and meat. The functionality and health of the mammary gland are directly correlated with milk production, as well as with the hygiene and quality of milk and dairy products. Mastitis is one of the main infectious diseases in dairy sheep. One of the candidate genes that affect milk production traits is the ATP-binding cassette sub-family G member 2 (ABCG2) gene. The ABCG2 gene, a member of the ATP-binding cassette family, transports cytostatic and xenobiotic drugs across the cytoplasmic membrane. The study was based on 1747 records from 387 head of dairy sheep of the Lacaune breed (139) and the East Friesian breed (248). The analysis was performed by means of polymerase chain reactions (PCR). Genomic DNA was extracted from blood. Phenotype data used in the study were provided by the Association of Sheep and Goat Breeders in the Czech Republic (ASGB). We typed all three genotypes: DD, DI and II. In the Lacaune breed, the frequency of occurrence of the major D allele was 0.694, and the minor I allele had a frequency of occurrence of 0.306. In contrast, in East Friesian sheep the frequency of allele D was 0.216 and that of allele I was 0.784. Mutation c.683-80_46del in the intron 5 region of the ABCG2 gene confirmed the effect on somatic cell count in the dairy sheep population observed in this study. Further studies are needed to evaluate this possible association in other sheep breed populations. Mutation c.683-80_46del in intron 5 of the ABCG2 gene could be used as a candidate gene for somatic cell count.