Introduction. In recent decades, questions the impact of universities on regional economic development and the search for the most effective mechanisms and instruments of cooperation of universities and regions attracts more and more attention from researchers and practitioners. Methodology of the study. In this article it was set the goal – to study the influence of Russian universities in the innovative development of the regions. To assess the impact of universities on the performance of innovative development of regions were used statistical data of Federal service of state statistics for 2010–2013. The factors characterizing the influence of the university, was chosen set of statistically observable on the financial performance of national research universities. To assess the level of innovation development of the region was used the method of integral rating analysis of innovative activity and knowledge production function model. Results. Analysis of the correlation of the analyzed regions of the Russian Federation shows significant differentiation parameters and dynamics influence the activities of national research universities in the innovative development of the region. By increasing the amount of funds they have received R & D contracts with businesses in relation to their total revenues to 1 million rubles, the level of innovation development of the region will increase by 4.8499 units, which indicates good prospects for the development of regions with the active collaboration of universities and business.