Under conditions of growing competitive pressure, a role of universities in the development of innovations at both national and regional levels increases. At the same time, there is a shift from the dominant cooperative ties between the state and the enterprises in an industrial society to the ties between the state and enterprises and universities in the knowledge society. This work performed characterization of Germany by the level of innovative development. 4 types of Regional Innovation Systems were identified: innovation core, strong business- innovators, clusters with high level of governmental support, innovation periphery. Further, the territory was investigated for the formation of the research and educational function of universities and 5 types of regions with different types of universities (leading, high, medium, underdeveloped and backward) were identified. An analysis of the laws governing university participation in innovation processes has shown that their innovation activity is formed under the influence of both the regional innovation environment and institutional factors. In the western part of the country, the nature of research activity of universities is driven mainly by their intensity of cooperation with businesses while in the eastern part it is determined by the level of state support for R & D.