DNA typing technologies make it possible to detect alleles and their frequencies in biochemical systems of proteins and enzymes, including specific PCR sequences, restriction enzymes and actually single nucleotide polymorphisms. The development of breed-specific SNPs is necessary for genotyping and mapping of associations with milk productivity traits, which will make it possible to identify the most valuable genotypes for their further use in selection and breeding work. The purpose of the study is to determine the allelic and genotypic frequencies, genetic diversity and polymorphism of hemoglobin (HB), ceruloplasmin (CP), posttransferrin (pTf), amylase (Am-1) and the receptor for vitamin D (calcitriol) (GS) to identify the relationship breed-specific features of their genetic structure. The results of the research revealed the influence of the breed of cows on their genetic structure according to the genetic-biochemical systems pTf, GS, HB, CP and Am-1. A clear influence of the genotype factor at the posttransferrin locus was observed, among the studied breeds of cows, on the manifestation of the content and amount of protein in milk. In addition, a probable effect of ceruloplasmin on the parameters of fat and protein in milk was established, depending on the breed of cows. The assessment of the genetic-biochemical system based on the amylase locus established a clear influence of the genotype on the manifestation of milk yield, milk fat and the amount of protein in milk. Thus, the use of polymorphism of individual loci of proteins and blood enzymes in the conduct of selection and breeding work will not only contribute to the improvement of breeding work, but also to the improvement of dairy cattle in general. Therefore, the perspective of breeding work with Holstein cattle should be the assessment of the diversity of the allelogen according to the polymorphic system of proteins and enzymes, which will allow to identify the best genotypes not only in terms of productivity, but also in genetic terms.