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One of the important questions for innovative environment development is social-economic institutions, which help to decrease transaction cost and risks in small and medium size enterprises (SMEs). Basic institutional framework is represented by a set of specific institutions, which form the innovation environment of the region and have an impact on the activities of the innovation system actors. The proposed set of institutions is divided into two groups: those institutions that directly affect the development of innovative environment and institutions, which influence is indirect, but nevertheless important. The result of analysis of institutions development of Tomsk region and five more innovation-oriented areas of the Russian Federation is given in the article.