The protein composition of goat milk differs between goat breeds and could present regional trends. The aim of this study was to comparatively analyze the protein composition of goat milk produced by the Alpine and Saanen breeds in northeastern Brazil and to evaluate the antibacterial activity of its protein fractions. SDS-PAGE, 2-DE electrophoresis and RP-HPLC analyses revealed the absence of αs1-casein in the milk of both breeds and no differences between the αs2-casein, β-casein, β-lactoglobulin and α-lactalbumin profiles. The amounts of soluble proteins and β-casein hydrolysis residues were higher in Saanen milk. Only the protein fraction containing the largest amounts of casein (F60–90%) inhibited bacterial growth, with MIC values between 50 and 100 mg/mL. This study describe for the first time three important points about the goat milk protein of two Brazilian goat breeders: absence of α-s1 casein in the protein profile, differences between the milk protein composition produced by goats of Alpine and Saanen breeders and antibacterial activity of unbroken proteins (casein-rich fraction) present in these milk.