Whey protein isolates (WPI) can be aggregated upon heating to create new functional properties (e.g. texture), which depend on aggregate size and structural properties. In industrial conditions, aggregates are obtained in continuous processes at high temperature (≥ 75 • C) in few minutes. When studying the kinetics of WPI aggregation at high temperature and under flow, one major issue is to develop a process in which heat transfer does not limit aggregation. To this end, we used a down-scaling approach in which a WPI solution flows in a heated capillary tube. We show that this process makes it possible to study both the kinetics of aggregation after few seconds and its dependence with the mean shear rate in isothermal conditions. The size and mass of aggregates and protein conformation were characterized by small-angle X-ray scattering and resonant mass measurement for a single physico-chemical condition (pH 7.0, 10 mM NaCl, 92 • C, 4 % w/w WPI) which led to sub-micrometric aggregates. Firstly, we report that the size of aggregates were three times larger than when produced in a test tube. Secondly, the size and mass of aggregates reached a steady-state value in a few seconds, whereas the kinetics of aggregation and denaturation had a characteristic time of few minutes. Thirdly, the shear rate had no significant effect on the size of the aggregates, or on the aggregation kinetics. We concluded that WPI aggregation at 92 • C is limited by a step of nucleation, and that the fact that aggregates produced in test tube were smaller is due to a slower thermalization.