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Milk samples of 39 lactating West African Dwarf does in selected households in Akinyele Local Government Area of Oyo State were analyzed to study the genetic polymorphism of α-lactalbumin and lactoferrin and their effect on milk fat content. Genetic variants of milk protein were detected by cellulose acetate electrophoresis; milk samples were processed to remove fat prior to analysis. The interpretation of electrophoretic migrations revealed the presence of two alleles in each locus studied. The two alleles A and B controlled three genotypes: AA, AB and BB. Homozygous genotypes AA and BB at the α-Lactalbumin locus was observed in 17 and 5 individuals representing 42.5% and 12.5% respectively and 11 and 6 individuals representing 27.5% and 15% at the lactoferrin locus. No significant effect on milk fat content was observed for the two loci studied.