First stage (0–6 mo) infant milk formulae (IMF) are designed to approximate the protein, carbohydrate, fatty acid and micronutrient composition of human milk. Protein profile of the formulation is a key consideration and whey protein is typically added to bovine skim milk to more closely mimic the profile in breast milk. The whey to casein ratio is increased from 20:80 in bovine milk to 60:40 in IMF. Consequently, IMF can exhibit lower in-process heat stability compared with bovine milk, partially due to the heat labile nature of whey and, in particular, β-Lactoglobulin (β-Lg). Recent research carried out at Teagasc demonstrated the effect of temperature, pH and concentration on aggregate formation from heat treated whey proteins. Techniques such as nuclear magnetic resonance (NMR), light scattering (LS) and SDS-PAGE were used to determine heat induced changes in matrices of varying complexity, from simple β-Lactoglobulin (β-Lg) solutions to model IMFs. NMR showed structural changes in β-Lg solutions were minimal at 62°C, however at 85°C, increasing protein concentration from 1 to 12% resulted in a more stable structure in some reactive regions. LS showed that aggregate size decreased significantly (P < 0.05) from 100 to 59nm on increasing the concentration during heating (85°C × 30 s) from 1 to 12%, while heat stability increased at pH values greater than 6.9. In more complex model 1st stage formulations, heat-induced changes in whey protein stucture were not only a function of concentration but were also influenced by the presence of casein, lactose and fat. A greater amount of unresolved high molecular weight aggregates (SDS-PAGE) were present when skim milk and whey protein were heated in-combination compared with when heated separately, indicating that the extent of aggregation is influenced by the presence of casein. Higher protein aggregation resulted in increased concentrate viscosity, reduced atomisation efficiency and increased finished powder particle size. The research highlights the role that aggregation of whey protein and subsequent interaction with casein has on in-process stability, which impacts on drying parameters and finished powder functionality.