Introduction: Research evaluation based on peer review is done to assess the quality of research. In this article, the peer review evaluation results of selected Iranian research centers are presented. Methods: A qualitative study was conducted through peer review with 106 and 15 Iranian professors from inside and outside the country, respectively. The evaluation was implemented in four areas of leadership, structure, research products, and impact. In this study, research centers with independent research budget lines and 12 top research centers during 2015-2018 were evaluated. Results: The most weaknesses in these research centers were in leadership (scattered work, island and parallel activities) and impact (inefficiency of knowledge utilization in transfer chains) areas, and the greatest strengths were related to knowledge production (quantitative and qualitative development in the number of published articles and citations). In the structural part, the lack of attention to technological activities, the lack of applicability of research, and inadequate physical space were the most important weaknesses. Conclusion: In the peer review method, the assessment of leadership, structure, and in particular, impact areas has a very important role in research quality promotion due to appropriate interactions with specialists and peers.