At present, the role and importance of science is increasing significantly, more and more attention is being paid to scientometric indicators in assessing scientific activity at all stages of the science management process, and the cost of scientific activity is increasing. The problems of assessing intellectual capital have always been in the area of special attention in Russian scientific and other organizations, including universities engaged in scientific activities — scientific institutions. The decree of the President of the Russian Federation from 07.05.2018 No. 204 “National goals and strategic objectives of the development of the Russian Federation for the period until 2024” approves these trends at the state level. Therefore, the task arose of developing a system of quantitative and qualitative indicators for assessing the effectiveness of scientific organizations in order to organize their productive work, increase their contribution to the development of the state, and increase the prestige of science. The external and internal factors determining the need for an objective assessment of intellectual capital are identified using the methods of comparative analysis, empirical research; the main indicators, the sources of information and their features have been analyzed. The proposed system of universal criteria, objective and subjective indicators for assessing the activities of scientific institutions, is becoming the foundation for both a comprehensive assessment and the basis for industry criteria.