Microfiltration and ultrafiltration were used to manufacture skim milks with an increased or reduced concentration of whey proteins, while keeping the casein and milk salts concentrations constant. The skim milks were heated on a pilot-scale UHT plant at 80, 90 and 120 °C. The heat-induced denaturation and aggregation of β-lactoglobulin (β-lg), α-lactalbumin (α-la) and bovine serum albumin (BSA) were quantified by polyacrylamide gel electrophoresis. Apparent rate constants and reaction orders were calculated for β-lg, α-la and BSA denaturation. Rates of β-lg, α-la and BSA denaturation increased with increasing whey protein concentration. The rate of α-la and BSA denaturation was affected to a greater extent than β-lg by the change in whey protein concentration. After heating at 120 °C for 160 s, the concentration of β-lg and α-la associated with the casein micelles increased as the initial concentration of whey proteins increased.