The aim of this study is to estimiate the associations between the ANXA9, FABP3, and FABP4 genotypes and the breeding value for milk production traits (yields of milk, protein, and fat, as well as protein and fat percentage) in 975 Polish Holstein-Friesian cows. The frequencies of genotypes and alleles were determined. Statistically significant relations between the ANXA9 SNP and the breeding value for fat content, as well as the FABP4 SNP and the breeding value for protein content were found. The results indicated that selection for the ANXA9 GG and FABP4 GG animals might contribute to an decreased fat content and increased protein content in milk, respectively, in Polish Holstein-Friesian cows. Although verification in the further studies is needed.