Medical science excellent centers have consistently sought to improve scientific status, expand the knowledge base, increase the number of expert researchers, create a dynamic environment, and promote a productive and effective international scientific network during the past several decades. In Iran since 1379, medical excellent centers joined the education and  research structure as the highest scientific institutions and now there are 50 excellent centers. The senior
management of the higher education system in the country is responsible for evaluation of these newly established scientific institutions. Assessment of these centers shows the quality of their activities, which can contributes to quality improvement through dynamic feedback for the planning and activity development. In order to perform this assessment, the Iranian Ministry of Health and Medical Education as an important part of higher education system designed a model of assessment and put it on its agenda in 2010 that was revised in 2015. This article aims to describe the process of developing the tools needed for this evaluation. The evaluation criteria has been developed based on “input”, “process” and “educational, research, and services outcome” indexes. This evaluation has been considered as a comprehensive one, because of including all aspects of management such as supply and training human resources, financing, providing equipment, process of empowerment and knowledge production as well as output in the field of education, research, industry and services. This scientific approach to the assessment and ranking of excellent centers makes them capable of being aware of their strengths and weaknesses. As a result, they can improve their scientific capacity and activities. 

Keywords: Excellent center, Assessment , Ranking