The objective of this study was to investigate genetic variability of CSN1S1 gene coding for alpha-s1-casein in goat populations raised in Southeastern Region of Turkey. Blood samples were collected from goats raised in Kilis(n=60), Sanliurfa (n=56), and Siirt (n=55) provinces of Turkey. From the blood samples DNA was isolated by using phenol-chloroform extraction. Genotypes of animals were determined by using polymerase chain reaction (PCR), allele specific PCR or PCR and restriction fragment length polymorphism methods. In Kilis and Sanliurfa populations CSN1S1 A*, B*, F and N alleles were observed, while in Siirt population only A* and B* alleles were found. Frequencies of A*, B*, F and N alleles were 0.375, 0.367, 0.017 and 0.242 in Kills, 0.632, 0.208, 0.009 and 0.151 in Sanliurfa and 0.782, 0.218, 0.000 and 0.000 in Siirt populations, respectively. CSN1S1 E and 01 alleles were not observed among the populations studied. Observed and expected genotype frequencies did not differ significantly (P>0.05). The results of this study suggested that there were sufficient genetic variability of CSN1S1 gene especially in Sanliurfa and Kilis populations in order to select individuals for different breeding purposes.