The aims of this study were to type genetic variants in the casein genes in Czech dairy goat population and to assess an association within genotypes group at the casein loci on the following milk production parameters: mean daily milk yield, protein yield, and protein production during 240-days milking in 389 animals of Czech mixed dairy goat breeds in first till third lactation. Different molecular techniques: AS-PCR, PCR-RFLP and PEA (SNaP Shot) were used to determine genetic variants. Molecular analysis confirmed that the F (0.622) allele at CSN1S1 locus was predominant compared to the A allele and prevalent genotype was FA (0.524). At CSN2 locus allele C was predominant (0.669) compared to A allele (0.331) and genotype AC (0.486) and CC (0.427) had similar appearance. Frequency of allele F and N was similar (0.478, 0.522, respectively) at CSN1S2 locus. Frequencies of allele B (0.765) and genotype BB (0.619) at the CSN3 locus were dominant in goat population. Associations between milk production parameters and casein gene polymorphism were investigated, and significant effects were found on protein content, at loci CSN1S1, CSN1S2, CSN3 (P < 0.001), and CSN2 (P < 0.05). Also, significant effect was found on protein production at 240d of lactation at locus CSN3. These results indicate that casein genetic polymorphism loci should be used as a molecular marker for marker-assisted selection (MAS) for improving of milk composition and protein production.