Polymorphism of caprine milk proteins was studied by capillary electrophoresis. Identification of casein (CN) fractions was effected by using isolated fractions from cation-exchange fast protein liquid chromatography. Genetic polymorphisms in caprine αs2-CN, αs1-CN, β-CN and κ-CN have been determined. κ-CN A and B, β-CN A and null, αs2-CN A, B and C, αs1-CN A, B, C and null, and other forms with intermediate and low αs1-CN content have been identified. The capillary electrophoresis method made it possible to analyse whole caprine milk using simple sample preparation and was rapid, automated and suitable for phenotyping studies. This method may also permit the quantitative study of different protein fractions.