Bovine skim milk samples with different phenotypes of kappa-casein (AB and BB; kappa-cn) and beta-lactoglobulin (AA, AB, and BE; beta-lg) were heat-treated at 90 degrees C for different times (1-10 min). The residual native whey proteins in the ultracentrifugal supernatants were determined by fast performance liquid chromatography using a MonoQ HR5/5 column at pH 6.2, and the loss of native beta-lg was recorded. The rate of heat-induced loss of native beta-lg, expressed as the inverted half-life (1/t(1/2)) of the reaction, was calculated. The reaction did not follow true first- or second-order kinetics, varying between the different genetic combinations. The highest 1/t(1/2) values were found in milk from cows homozygous for kappa-cn B or beta-lg B. The same was true after adjustment for differences in casein number. Both the beta-lg and kappa-cn genetic variants were found to significantly influence the heat-induced aggregation reaction; with beta-lg having the greatest effect. Statistical analysis showed that the two loci for beta-lg and kappa-cn accounted for more than half of the phenotypic variance in the experimental groups.