The paper presents the methodological bases for assessing research efficiency. In accordance with the existing regulatory framework, research efficiency (both personified and institutional as a whole) is assessed on the basis of common indicators. The use of the unified system of indicators for all types of assessment allows one to get an idea of an organization’s human capacity, its qualities, capabilities, and reserves. Taking into account that measures aimed at improving research efficiency and quality are determined by the performance indicators of employees, there is a need for their systematic monitoring with the tools and methods based on up-to-date management technologies. Personified assessment of a scientist’s activity is a complex system that is implemented through two successive and interrelated processes: certification (CE) and effective contract (EC), which are based on the score-rating method. According to the rating scale adopted by an organization, each quantitative and qualitative indicator of research efficiency is assigned a certain number of points. They are summed up for a certain length of time when determining the personal rating of a researcher. Synchronization of the quantitative and qualitative indicators of research efficiency, which are used in the implementation of CE and EC, facilitates the analysis of the findings. To evaluate the research activities of an organization and to determine the performance efficiency of a particular scientist, it is necessary to implement procedures for collecting, recording, and monitoring the results of their activities. If an automated accounting system for research results is unavailable, their analysis and comparison with indicative indicators for each employee are a complex and time-consuming process when monitoring within CE and EC. The experience of the National Medical Research Center for Preventive Medicine (NMRCPM), Ministry of Health of Russia, shows that the use of an automated information analytical system makes it possible to optimize researchers’ activities, to become a promising and competitive organization, and to achieve leadership positions in its reference group. According to the Russian Science Citation Index, NMRCPM, Ministry of Health of Russia, is among the three leaders in the number of citations per author and among the top ten leaders in the number of citations per publication among the 52 institutions subordinate to the Ministry of Health of the Russian Federation.