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A 3D fouling model for milk pasteurizer using plate heat exchangers (PHEs) was developed using the computational fluid dynamics (CFD) approach. Based on the hydrodynamic and thermodynamic performances of PHEs in 3D environment, the chemical reaction equations employed for protein denaturation and absorption onto the stainless steal surface were coupled using the FLUENT software. The 10-channel PHE system with both counter-current and co-current flows was applied to validate the model by visualizing and quantifying the milk deposit formulated in the fluid channels. The predicted mass deposit values were in good agreement with the experimental data with the prediction error of 0.01 g or 1%. The simulation results based on new PHE system, designed for the uniformity of flow distribution, showed the deposited mass could be reduced to 1/10, compared to the current system under the identical energy basis. Although the intensive computational efforts required, the 3D fouling model was validated as an effective tool for design of new plate shapes and corrugation profiles optimized for minimizing milk fouling.