The aim of this study was to identify polymorphisms in the bovine genes encoding CSN1A1 and CSN3 caseins and analyse the structure of population of Slovak Spotted cattle. Subsequent analysis was carried out to estimate the effect of both polymorphisms on long-life milk production traits. The genomic DNA was extracted from totally 180 blood samples. All of analysed animals were genotyped by using the PCR-RFLP method. In population the prevalence of homozygote animals was found. For CSN1A1 gene the BB genotype was noted as predominant. In terms of CSN3 gene the genotype frequencies was more balanced. The most frequent genotype were AA. The population genetic indices signalised the decrease of genetic variability in population mainly for CSN1A1 gene. Except F_IS index, each of parameter reflected the high proportion of BB homozygous individuals in population. The values of observed and expected heterozygosity for CSN3 gene indicated similarly the prevalence of homozygote individuals in population, but the decrease of heterozygosity was not so high. The effect of polymorphisms on production traits was tested based on the GLM procedure. In case of both SNPs we were able to describe the variability of analysed traits on 95%. The study results clearly indicated the positive effects of CSN1A1^BB and CSN3^AA genotypes in order to improve the milk production traits in Slovak Spotted cattle. In addition, the statistical analysis confirmed the key role of casein in milk production and its composition.