The aim of this work was to evaluate the variability of the s1-casein locus in the endangered Girgentana dairy goat breed in order to define genetic improvement and conservation program for this breed. The study was performed on 200 dairy goats by means of different PCR protocols. The most frequent alleles were A (0.590) and F (0.290) followed by B (0.065) and N (0.047). CSN1S1 E allele was identified with a very low frequency (0.008). The most common genotype was AF (0.365) followed by AA (0.340). The high frequency of the strong genotypes is associated with the production of milk with high fat and protein content and with optimal technological properties. In Girgentana goat breed, the CSN1S1 genotype information could be utilized in selection strategies for milk protein content and milk yield, in order to select genetic lines for the production of “drinking milk” using weak and null genotypes, and for niche products using strong genotypes.