The application of Petri nets for modeling automated target recognition is proposed. This theory will permit the reformulation of automatic target recognition algorithms and paradigms into a modern scientific model that incorporates all the details of a realistic, complex scene. Petri nets have recently been studied and applied to a variety of applications. Their use permits the modeling of both information flow and physical material flow in an overall system model which clearly shows constraints, influences of variables on system performance, and results in a system which can be realized in hardware under software control. This proposed theory promises to revolutionize the model of command, communication and control currently used by integrating the three functions into one overall control system model. The theory has been demonstrated on two systems and the automatic target recognition problem is an ideal test bed for further study.