The aim of the study was to determine the frequencies of B1, B2, B3 and E alleles of the CSN1S1 gene and their effects on milk yield and composition in the Saanen goat breed. Milk samples were collected to identify milk composition with Fourier transform infrared (FTIR) spectroscopy. The polymerase chain reaction -restriction fragment length polymorphism (PCR-RFLP) method was used to characterize the alleles of CSN1S1 gene. The allelic frequencies of the B1, B2, B3 and E alleles were 0.927, 0.073, 0.390, and 0.272, respectively. B1 and B2 alleles did not affect milk yield and composition. B3 allele had significant effects on protein, fat, total solid (TS), solid not fat (SNF), casein and lactose percentages, but not on lactose yield. E allele significantly influenced fat and TS percentages of milk in the Saanen goat breed. The protein (3.58%), fat (3.83%), TS (12.06%), SNF (8.60%) and casein percentages (2.80%) were higher in B3/B3 goats than in B3/NB3 (NB3: non-B3) and NB3/NB3 goats. For E allele, NE/NE (NE: non-E) goats displayed higher fat (4.06%) and TS (12.42%) percentages of milk than their E/E and E/NE counterparts. As a result, the potential for improving milk composition by selecting for B3 and E allele may be significant in Saanen goats.