The paper describes the proposed procedure for estimating genomic breeding values by a multi-trait model, including exterior traits and the average number of somatic cells per lactation. In particular, the procedure increases the reliability of estimates of breeding values using the direct manifestation of the disease and the traits that are genetically correlated with it. Genomic breeding values were estimated at a population of 62,933 Holstein cows (from H75 above), reaching 101,261 lactations with a lactating incidence of clinical mastitis (KM) of 19.50%. Values of linear type score were known in 49,886 cows for udder depth, suspensory ligament, udder width and udder as an overall characteristic. The estimation method was a linear multi-trait animal model with a single-step genomic prediction method. The reliability of the estimation of breeding values has been increased. It has been confirmed that the breeding values for KM reflect phenotypic ratios in KM prevalence in the population. A higher incidence of KM has also been associated with other diseases such as ovarian cyst syndrome.