In the context of identifying intrinsic time temperature integrators (TTIs) for evaluating heat processing of milk, the extent to which milk fat content has an effect on alkaline phosphatase (ALP) and lactoperoxidase (Lpo) inactivation and on β-lactoglobulin (β-lg) denaturation kinetics was studied. Inactivation and denaturation kinetics were analysed in whole, semi-skimmed and skimmed milk. In previous experiments (isothermal and non-isothermal heating conditions), heat inactivation of ALP and Lpo and heat denaturation of β-lg were found to follow first order kinetics. This allowed experimental design to be simplified. Data analysis was performed by non-linear regression and results were evaluated by construction of joint confidence regions. The possible effect of milk fat was illustrated by temperature time tolerance (TTT-) diagrams. Although initial ALP activity was lower in skimmed milk compared with semi-skimmed or whole milk, kinetics were comparable and fat content did not seem to substantially affect the ALP test result for pasteurized milk. Unlike ALP, Lpo inactivation and β-lg denaturation kinetics differed significantly in milk with different fat content. Differences between Lpo inactivation kinetics were relatively small and acceptable in the context of quantifying the process impact. Denaturation of β-lg, on the other hand, seemed to be enhanced at higher milk fat content (>72 °C).