The role of scientific research institutions in the development of the region’s certainly much more difficult to determine the specific development in the innovative aspect as a factor in the competitiveness of the region, this article examines the role of research institutions is to develop an innovative component of the region and provides a system for performance evaluation. Theoretical analysis. Innovative development of the region is represented in the article as a system, is used both a systematic approach to the study of this aspect. Through a series of functions of the system examines the factors that contribute to the implementation of its system functions and tasks. In this article are allocated and subsystems overall structure of the theoretical division, and an example of combining these sub-systems within an organization in practice. Results. The result of the study is to construct an algorithm of sequential actions in the evaluation of innovative building and development in general. Application of theory to practice through the unification of the four sub-regional innovative development within an organization and classification proposal of indicators to assess the development potential of the region.