Genetic polymorphisms of casein have received a considerable research effort for many years because of its potential effect on milk composition. Milk composition, specifically protein content, differs quantitatively and qualitatively among species and also among breeds and individuals. Sicilian goat breeds seem to be an interesting model since they have never been under a selection program, and therefore may carry unique casein polymorphisms. Moreover, the importance of goat milk in infant diets is growing probably because goat milk in some cases is less allergenic than cow milk. It is important to evaluate the genetic polymorphisms at the CSN1S1 locus in the populations of interest, like the Girgentana or Maltese goat breeds, because caseins are considered as the main cause of allergic reactions. Moreover CSN1S1 polymorphisms have been associated to different levels of this protein expression in milk. The goal of the present research was twofold 1) to genotype CSN1S1 locus, and 2) to type casein protein polymorphisms in two Sicilian breeds, Maltese and Girgentana. Blood and milk samples were obtained from 400 animals (200 of each breed) located in four different flocks. DNA was extracted from leucocytes and CSN1S1 polymorphisms were detected by PCR followed by restriction fragment length polymorphism (PCR-RFLP), and by allele specific PCR (AS-PCR). PCR and digestion products were analyzed by electrophoresis in 3% agarose gel stained with ethidium bromide after exposure to ultraviolet light. Milk samples, from the same individuals, were analysed for protein expression by isoelectrofocusing (IEF). IEF was carried out over a 2.5- 6.0 pH gradient. Protein separation was performed in a polyacrylamide gel, and stained with Coomassie Brilliant Blue G250. Results showed a high percentage of A and B alleles (considered strong alleles), but also the presence of weak (F) and null alleles (N) was found in both breeds. The results may have practical implications to plan a selection program given that animals with allele A and B might be useful for cheese production since these animals express more casein than those carrying F or N alleles, and animals that do not express casein might be beneficial for hypoallergenic milk production.