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The objective of this study was to develop the evaluation software of microbiological safety of food during microwave heating. The information of thermal inactivation kinetics of potential pathogens in food material is essential for proper thermal process design and operation. Mathematical model was developed to predict the thermal inactivation of microorganisms, Salmonella sp. and Listeria innocua, in chicken breast meat during microwave heating. The model was based on three-dimensional heat and mass transfer with appropriate boundary conditions, and microbiological destruction model. The model was solved numerically using the control volume method.