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The article is devoted to the issues of optimizing and the innovational development managing in Russia's regions based on the statistical methods and the theory of decisionmaking. The existing innovation indices were studied and their benefits and drawbacks are given. We offer the methodology of the system estimation of hierarchically structured innovative activity indicators, which is peculiar for the preliminary statistical analysis of the evaluated parameters. It is indicated that the majority of the characteristics of innovation process in the Russian Federation obeys log-normal distribution, which implies the logarithms of empirical data for the correct use of the mathematical tool of the theory of decision-making and obtaining results of easily comprehensible form. We clustered Russian regions into four clusters which represent the scientific and technical potential, the level of innovation activity and the state of innovations' activity sphere. The results of the clustering have enabled us to define three leading regions which stand out due to their high-quality innovation activity. What is common for many other regions is that the ineffective unleashing interferes with their high innovation potential. Thus, it is crucial to develop the infrastructure of the commercialization of innovations in the Russian regions. According to the cluster peculiarities we offer the ways to increase the innovational development effectiveness in regions based on the received results.