The effects of the flow behaviour at different temperatures on whey protein isolate (WPI) suspensions, pure or mixed with xanthan, have been investigated at pH 5.4. The experiments were performed in a continuous rotor/stator device? on the pilot-scale, using different rotational speeds and rotor geometries. The effects of a defined shear flow in a concentric cylinder system were compared with the shear and elongational flow resulting in a geometry with two scraping blades. The aggregation was studied by means of a phase inverse light microscope and quantified by particle laser diffraction measurements. The suspensions were rheologically analysed by a steady stress sweep. A decrease in aggregate size was found with an increased rotational speed, independent of temperature and rotor geometry. For the pure suspensions, the increase in rotational speed from 100 to 500 rpm, in the absence of scrapers, was accompanied by Taylor vortices. These changes in flow behaviour resulted in a dramatic decrease in aggregate size for the suspensions close to denaturation at 70 degrees C. The rotor geometry also influenced the aggregate size. At 70 degrees C, smaller aggregates were formed in the presence of scrapers compared to in the absence of scrapers, while below denaturation at 50 degrees C, the opposite behaviour was found. The viscosity of the processed suspensions was lower compared to that for an unprocessed sample. The processed sample showed shear thickening behaviour. In the presence of xanthan, the effects of temperature and flow behaviour on the WPI aggregation were similar but less pronounced than those in the pure suspensions. This indicates that xanthan inhibits the effects on the WPI aggregation. When scrapers were attached to the rotor, WPI aggregates with a tendency to a long and rod-like shape were formed. These shaped aggregates were explained in terms of the flow behaviour and the pseudoplastic nature of xanthan. All mixtures showed this pseudoplastic behaviour, independent of process history.