The advantage of LightCycler analysis (LCA) is based on speed, efficiency, and safety (absence of hazardous chemicals). At present, work is in progress to analyze further polymorphisms within CSN2 locus to allow the simultaneous detection of all the known genetic variants of the gene and exploit all the potential of the LCA technique. In this study, a protocol was developed for rapid genotyping of A and C variants at the CSN2 locus in two goat breeds reared in the Czech Republic validated (White Shorthaired and Brown Shorthaired goat). Monitoring of CSN2 variability in the goat breeds indicated the predominance of the C allele. In both breeds, CSN2A and CSN2C showed almost similar frequencies.