Processing of milk results in structural modifications of proteins creating a foundation for various interactions. The present study aimed at identifying the effects of simulated processing conditions, the combination of temperature and shear, on native proteins in raw skim milk. The temperatures chosen (72 and 140 °C) were combined with selected shear rates (0, 500, or 1000 s-1) during processing. Impact of shear appeared temperature dependent, but it induced either reversible or irreversible changes in the secondary structure of milk proteins at all temperatures. Increase in shear may result in reversible structural modifications at 20 °C, while it could contribute to fragmentation of hydrophobically-linked protein aggregates at 500 s-1 and also reformation at 1000 s-1 during heating at 72 °C. The shearing at 140 °C appeared to enhance the formation of protein aggregates primarily by hydrophobic interactions, as well possibly thiol/disulphide interactions to a lesser extent.