Abstract. The aim of the study was to compare the frequencies of protein polymorphisms in milk produced by cows with various proportion of HF genes within their genotypes, managed in two farms.

Frequency analyses of beta-lactoglobulin (BLG) and three casein fractions (CSN1S1, CSN2, and CSN3) in individual genetic groups of animals were carried out in milk of 342 cows. Also, milk content of casein and whey proteins was assayed.

The highest level of casein was found in farm B, in all the genotypic groups of cows, while the proportion of whey proteins in milk was highest in farm A, in the genotypic group of cows with 25% to 50% of HF genes. As far as the remaining groups of cows are concerned, the level of whey proteins was equal in both studied farms.

A genetic differentiation of polymorphisms in milk protein was found in the analysed farms. Frequency of kappa-casein B (CSN3 B) genetic variants, which are desired in processing, was higher in farm A.