Protein type and/or heat treatment pre- or post-homogenisation can affect the physical stability of infant formulations during manufacture. Previous research has described the use of α-lactalbumin addition in infant formulae, but has not demonstrated the effect of heating pre- or post-emulsion formulation during processing. The objective of this study was to evaluate the effect of both of these parameters. Three batches of model 1st-stage infant formula containing differing whey protein ratios (60:40 whey: casein with α-lactalbumin content 12, 30 or 48% of total protein) were prepared. Each batch was split; one half receiving heat treatment pre-homogenisation and the second half homogenised and then heat treated. Emulsion stability was determined by size exclusion chromatography, SDS-PAGE, particle size and viscosity measurements. There was a significant (P < 0.05) reduction in the formation of large soluble aggregates upon increasing α-lac concentration in emulsions heat treated either before or after homogenisation. Heat treatment of formulations post-homogenisation resulted in a higher (P < 0.05) D.v09 within the particle size distribution; increasing α-lactalbumin concentration to 30 or 48% significantly (P < 0.05) reduced the D.v09 within the particle size distribution in these emulsions. The viscosity of concentrates (55 % total solids) containing the 12% α-lactalbumin, heat treated post-homogenisation, was significantly greater (P < 0.05) than the equivalent emulsion heat treated pre-homogenisation; increasing the α-lactalbumin concentration to 30 or 48% significantly (P < 0.05) reduced viscosity. When the α-lactalbumin content was increased to 48% as a percentage of the total protein, heating before or after emulsion formation had no effect on concentrate viscosity. The findings demonstrate the importance of thermal denaturation/aggregation of whey proteins (and in particular, the ratio of α-lactalbumin to β-lactoglobulin) prior to homogenisation of infant formula emulsions.