In this work we identify 16 key indicators to evaluate the performance of healthcare research organizations. These indicators comprehensively characterize such aspects of performance as research output and relevance, human resource development, integration into the international scientific community, distribution of scientific knowledge, promotion of the prestige of science, and resource provision. Below, we review the existing classification of medical research institutions and their key features. We present the results of the comprehensive performance evaluation of healthcare research organizations. We demonstrate the significance of the proposed indicators that accurately reflect the output and relevance of scientific research and stress that indicators currently used for performance evaluation are insufficient. We also emphasize the need for a systemic approach to personnel capacity assessment and confirm the importance of additional evaluation criteria that amount to 37.5 % of all key indicators.