Milk samples from 237 Holstein-Friesian (HF) and 177 Simmentaler cows in six herds were typed for genetic variants of aS1-, b– and k-caseins (Cn) and b-lactoglobulin (-Lg) using ultrathin-layer polyacrylamide isoelectric focusing in the presence of carrier ampholytes (3-10 pH). The frequency distribution of genetic variants of all four milk protein systems was different in HF and Simmentaler. In addition, milk production traits of the dairy cows were compared according to the genetic variants of each milk protein fraction. Milk yield was significantly influenced by k-Cn (genotype AA > genotype AB) and b-Lg (AB > BB > AA) in HF, while in the Simmentaler milk yield was significantly associated with b-Cn (A2A2 > A1B > A2B > A1A2 > A1A1) and k-Cn (AB > AA > BB). In terms of protein content aS1-Cn was significant (BC > BB) in HF, and aS1-Cn (BC > BB), b-Cn (A1A1 > A2A2 > A1B > A1A2 > A2B), k-Cn (AA > AB = BB) as well as b-Lg (BB > AA > AB) were significant in Simmentaler. The effects of milk protein genetic variants on milk fat content in HF were not significant, while in Simmentaler this trait was significantly affected by aS1-Cn (BC > BB), b-Cn (A1A1 > A1B > A2A2 > A1A2 > A2B) and b-Lg (BB > AA > AB).