At present, innovative sphere is becoming the main factor of economic growth, affecting the structure of social production, altering the economic organization of society, stabilizing the social situation in the country. Innovative development of countries is caused by the necessity of a constant increase and maintenance of the level of competition on the world market. In order to make countries competitive, it is necessary to create the infrastructure conditions for innovative interaction and to establish the relationship between science and the business community. This factor highlights the need for the formation and development of innovative universities. Consequently, the development of innovative universities, with a broad internal information space for knowledge transfer, enables the formation of the environment and infrastructure that support innovation in small and medium-sized businesses. The purpose of this article is to consider the characteristics of functioning of the institutions in innovative sphere and justify their relevance to the development of innovative economy. In this paper we complete the following tasks: considere innovative activity of organizations in some regions of the Russian Federation and the index of innovative development of regions for 2014, analyze the organizations that operate in the innovation infrastructure of the Southern Federal District. Methods of comparative analysis and systematization were used to conduct the study. The work is a comprehensive overview of the innovative provisions of the Russian Federation. The paper substantiates the necessity of the development of universities as institutions for development in the innovation sphere and suggests the measures to further improvement of the innovative development institutions system in the Russian Federation. On the basis of the study it is concluded that one of the regional institutions for development are universities and it is necessary to provide the relationship between business and authorities to make sure they function efficiently.