Considering microwave (MW) heating as a viable alternative for in-shell pasteurization of eggs, after the simulation of the MW heating process by using a finite element model, process optimization was carried out to determine the most effective procedure and design for the process. The varying parameters obtained by using different modeling techniques for MW heating of in-shell eggs were optimized. Laboratory-scale experimental trials were conducted to test the validity and effectiveness of the optimized parameters. The optimal parameters set forth were found to be more efficient in terms of heating time and uniformity. MW heating appeared to be a viable alternative for the pasteurization of in-shell eggs. Copyright © 2011 John Wiley & Sons, Ltd.