The genetic polymorphism of the CSN1S1 (casein alpha-S1) locus was investigated in two endangered Czech goat breeds (White Shorthair and Brown Shorthair). These breeds are kept mainly for their good dairy performance. Genetic characterization of the CSN1S1 locus contributes to the knowledge of the genetic structure of these two endangered breeds. The study was performed on 498 goats (333 White and 165 Brown Shorthair goats) by means of different polymerase chain reactions (PCR). We detected A* (associated with normal content of protein), E, F and 01 alleles. The analysis showed a prevalence of CSN1S1 F (0.658; 0.597) and CSN1S1 A* (0.269; 0.303) alleles. In both breeds, the frequency of occurrence of E and 01 alleles was very low: E (0.054; 0.085) and 01 (0.019; 0.015), respectively. No population followed the Hardy-Weinberg equilibrium, the value of polymorphic information content (PIC) being 0.426 in White and 0.472 in Brown Shorthair goats. Moreover, the test of population differences (P = 0.130) showed no significant differences between White and Brown Shorthair goats. This genetic peculiarity makes the preservation of the population of both breeds worthwhile.