This paper represent part and core idea of doctoral dissertation, which was published and presented in Faculty of Mechanical Engineering, University of Montenegro. The paper point out many years experience from research in field of expert systems, business processes performance improvement, quality management systems and business excellence. The main objective is to develop intelligent system that will be based on the level of fulfillment of the requirements of ISO 9001 and give recommendations to improve the performance of business processes in terms of achieving business excellence (according European Award for Business Excellence) and achieving financial improvement. This should be an innovative approach which should make significant advantages of organization and their competitiveness. The main subjects of research are: the certified companies, their orientation to innovation as well as the development and implementation of innovation. For this research we use analogy between human body function and organizational activities. This system was tested in a one successfully organization and proved to be as efficient and effective.