Research is the tool for developing and extending the borders of the science and knowledge. As authorities of the research through administering and conducting practical, developmental, and fundamental researches, the research organizations (universities and research centers) extend the borders of the science and knowledge in all fields and offer some integrated solutions for the challenges facing the human. Nowadays, the periodical study on the performance of the research centers is an inevitable necessity in order to identify the effective factors on the performance appraisal of the relevant research centers. This study aims to identify the effective indices on evaluating the performance of the research centers. In this regard, we first distributed a questionnaire and analyzed the results and reached to 45 indices as the most important ones. Then we inserted these 45 indices into a final distributed questionnaire. To analyze the data and reduce the variables, we used factor analysis. Accordingly, 10 factors were identified as the most important factors in evaluating the research centers. These factors are as follows in order of their importance respectively: 1) scientific products; 2) achievements and awards; 3) research plans; 4) effectiveness; 5) scientific activities; 6) research resources and facilities; 7) commercialization and revenue; 8) management and organizational structure; 9) funds and credits; and 10) human resources.