Abstract Samples of cheese whey or acid casein whey obtained from commercial plants during the different stages of whey protein concentrate (WPC) manufacture were analyzed for protein composition and the extent of protein aggregation. Protein composition was determined by size exclusion chromatography (SEC) and electrophoresis, while the degree of protein aggregation was determined through the changes in molecular weight distributions monitored by SEC combined with multi-angle laser light scattering. The results show that there were some differences between the compositions of protein between the two types of wheys with the acid casein whey also containing lower proportions of “soluble” aggregates than the cheese whey. Ultrafiltration/diafiltration processes caused a removal of the non-protein, low molecular weight components, but had no significant effect on protein composition and aggregation. Evaporation and subsequent spray drying of the ultrafiltered retentates caused no significant changes in any of the whey protein components. Differences in functionality of WPC products are probably more related to modifications of proteins and other components caused by the processes that are used in cheese or casein manufacture rather than to the WPC manufacturing process.