The aim of the study was to analyse the dependence between P35Q and K468R polymorphism in the butyrophilin gene (BTN1A1) and somatic in milk in cattle. The experiment was conducted on a population of 214 jersey cows. Genotypes of the animals were determined using PCR-RFLP. The following allele sequences were found: P35Q – 085 (A) and 0.15 (C); K468R – 0.66 (A) and 0.34 (G). The association analysis was performed for the whole investigated population and with the division into age groups (primiparous and multiparous cows), and taking into consideration the stage lactation (the first, the second and the third 100 days). In case of mutation K468R, milk homozygous AA animals was characterised by the higher somatic cell count. Differences with the highest significance (p≤0.01) were found between genotypes AA and AG in the group of multiparous cows, especially in the initial perid of lactation. In the population of primiparious cows the effect of polymorphism K468R was much lower. A significant difference (p≤0.05 was observed only between homozygotes AA and GG in the first stage of lactation. An analysis performed for polymorphism P35Q did not show significant association with somatic cell counts in milk of cows.