This paper describes the procedure for estimating genetic parameters and genomic breeding values (GBV) for resistance to ovarian cysts in Holstein dairy cows. The genetic evaluation was performed using a linear animal model, the model equation included fixed effects of parity, herd, season and year of calving and random effects of animal, permanent environment and residual. SNP genotypes of 9,466 individuals determined on a 50K Illumina bovine bead chip were entered into the estimation. The coefficient of heritability was 2.5%. Follow-up weighted ssGWAS confirmed a highly polygenic nature of ovarian cyst. However, we detected some regions on BTA1, BTA12, BTA17, BTA19, and BTA29 that might be involved in the genetic determination of this reproductive disorder.