Eggs are possible hosts and transporters of pathogenic microbes such as Salmonella enteritidis as it contains higher nutrition. Heat pasteurization is the suitable method for reducing these pathogens, but the important functional properties of the eggs are exaggerated because of the protein denaturation. Based to various laboratory experiments, Finite Difference Time Domain (FDTD) and Finite Element Models (FEM) were created to simulate the electric field and power distribution in the egg constituents by considering the complex shape, dielectric properties and heterogeneous composition of the in-shell egg. In this paper, an effective optimization technique has been used to optimize the heating parameters. Genetic Algorithm has been used in this proposed approach. This can be helpful to improve the design and development of an industrial microwave in-shell eggs pasteurization unit. Experimental results show that the proposed technique for egg pasteurization results appeared to be better and the time required also reduced which can support the reduction in power consumption. © EuroJournals Publishing, Inc. 2012. © 2014 Elsevier B.V., All rights reserved.