The 4 casein loci were evaluated as haplotypes in 2 dairy goat breeds kept in the Czech Republic. Analysis of 41 White Shorthaired (WSH) trio families and 44 Brown Shorthaired (BSH) trio families revealed 14 and 20 haplotypes, respectively. Twenty-two different combinations of these alleles (casein haplotypes, in the order CSN1S1-CSN2-CSN1S2-CSN3) were found. For the WSH breed, the most common haplotype was FCFB (0.260), whereas for the BSH breed, the most common haplotype was FCFA (0.217).The information on the haplotype variability in both breeds could be used in breeding programs aimed at preserving biodiversity or selecting animals for specific protein production and cheesemaking.