the strategy for eliminating harmful mutations in the Holstein breed includes genetic monitoring of the prevalence of hidden hereditary anomalies using molecular genetic methods. Currently, there is a tendency to increase the number of hereditary diseases in highly productive breeding animals due to intensive selection and inbreeding. The aim of this study was to develop new and improve existing molecular genetic methods for diagnosing carriers of fertility haplotypes HH3, HH5 in Holstein cows and to study the incidence of these diseases. Diagnosis of heterozygous carriers of the mutation in the coding part of the SMC2 gene was carried out using the tetra-primer ARMS-PCR reaction, the sequences of external and internal primers were determined using the Primer 1 program. Allele-specific primers were used to detect carriers of the deletion in the TFB1M gene, the sizes of the PCR product in homozygous healthy animals 442 bp, in heterozygous carriers 442 bp. and 256 b.p. According to the results of genetic monitoring in the study population, the frequency of heterozygous carriers of the HH3 fertility haplotype was 3.23%, HH5 - 8.35%. It is recommended, in order to control the risk of morbidity of breeding stock with hereditary anomalies, to carry out genetic screening of breeding stock of dairy farms with the coverage of diagnostic tests ranging from 10% to 20% of the total livestock.