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The high-temperature short-time (HTST, 72 °C, 15 s) pasteurization of human milk (HM) has been proposed as an alternative to the Holder method (HoP, 62.5 °C, 30 min), to increase the preservation of bioactive compounds. We have investigated the impact of HTST and HoP pasteurization on the gastrointestinal kinetics of human milk, using a dynamic in vitro system in a preterm newborn model. An increased protein aggregation on the surface of fat globules following pasteurization, albeit to a lesser extent in HTST than in HoP, was observed.