The pertinence of the study stems from the need to develop the economy in a new direction according to the innovative model. The basis for an innovative economy is the development of innovative systems, including the subjects that give rise to inno- vations and the supporting infrastructure (innovation institutions). It is the latter that influence the development and dissemination of innovative processes. However, in studies on innovation systems, the issue of the effectiveness of innovation institutions is not considered separately from the entire system. In this regard, in this study, the goal is to evaluate the effectiveness of the activities of innovation institutions in the Khabarovsk Territory, as well as to determine the prospects for increasing the influence of educational organizations of higher education on the effectiveness of the re- gional innovation system. Methods: analysis of statistical data, classification and typification. The information base of the study was data from reports on the implementation of the state program prepared by the Ministry of Investment Development and Entrepreneurship of the Khabarovsk Territory, Rosstat and the Ministry of Education and Science from the statistical form No. HPE-1, HPE-2. As a result of the assessment of the effectiveness of innovative institutions in the Khabarovsk Territory, it was found that there is a duplication of functions in different subjects, while the effectiveness of their activities is reduced (fewer innovative projects, the amount of funding for innovative developments is reduced), a weak relationship was found between the perfor- mance indicators of university and labor resources, indicators of science and innovation. This indicates the inefficiency of the constructed interactions with other innovative institutions.