The accuracy of genomic breeding values (GEBV) for clinical mastitis (CM) of Czech Holstein cattle was analysed. The single-step genomic method and mixed genomic reference populations were employed. Dataset included 92,388 Holstein cows and 160,426 lactations. CM lactation incidence was 19.05%. Cows calved between 2017 and 2022 in 119 herds. A total of 4,969 Holstein sires and 35,814 Holstein females were genotyped. Three genomic matrices were used, two of them encompassing females. The linear animal model with repeatability included fixed effects of herd-year-season and parity-age at calving. The highest average accuracy of GEBV occurred for genotyped cows. SD of GEBV accuracy for bulls was significantly higher than these for cows. The accuracy of genotyped cows with health phenotypes ranged from 0.06 to 0.51. For the genotyped bulls born in 2021 and 2022, the maximal accuracy was 0.37; for genotyped heifers, the maximal accuracy was 0.42. The highest average GEBV accuracy occurred for the reference population with genotyped bulls and genotyped cows with phenotypes. The average accuracy for the young genotyped bulls increased by one percentage point when phenotyped cows were considered in the reference genomic population. The cow‘s GEBV accuracy benefited from including their genotypes in the prediction. It has been confirmed that due to the expansion of the genomic reference population to include a group of genotyped cows with phenotypes, the individual accuracy of GEBV for CM had increased.