Individual mid-lactation milk samples were collected from 116 cows of the Swedish Red and Swedish Holstein breeds with known genotypes of beta-casein, kappa-casein and beta-lactoglobulin. Detailed milk protein composition and allele-specific expression of beta-casein, kappa-casein and beta-lactoglobulin proteins in milk were analysed using reversed-phase high-performance liquid chromatography. Aggregate beta-/kappa-casein genotype was significantly associated with the kappa-casein concentration in milk. The lowest kappa-casein concentration was found in milk of cows with genotypes including kappa-casein E (A(1)A(2)/AE, A(1)A(1)/AE) and also A(2)A(2)/AA milk, whereas highest levels were associated with genotypes including kappa-casein B. Casein number was positively and concentration of beta-lactoglobulin negatively associated with the beta-lactoglobulin BB genotype. In heterozygote cows, beta-casein A(1) and beta-lactoglobulin A proteins were found at higher concentrations in milk compared with the protein variant encoded by the alternative allele at these loci, whereas kappa-casein A and B variants were found at similar concentrations in heterozygote AB cows.