Ovarian cysts are a common cause of reduced fertility or infertility in dairy cows. Among other measures (management, nutrition, etc.), their incidence can be influenced by breeding. A prerequisite for selection is the estimation of genetic parameters and breeding values for resistance to ovarian cysts. A univariate animal model with fixed effects of herd-year-calving season, lactation order and random effects of direct additive genetic effect of the individual and the cow’s permanent environment were used for the evaluation. Estimated heritability was low (2%). SNP genotype data were included in the estimation of breeding values, and the effects of genomic matrix adjustments (inclusion of cows with phenotype, inclusion of young individuals without phenotype) on the reliability of breeding values were compared.