Approaches to state support of innovative entrepreneurship through business development institutions are considered. The purpose of the policy of stimulating innovation activities of small and medium-sized enterprises as innovation-based economic growth is determined. Theories of innovations and concepts of technological structures are considered. The most important directions of support of small and medium-sized innovative enterprises are revealed: formation of state and regional innovative policy, programs of support of small and medium-sized business, effective functioning of institutes of development. Business development institutions are a state tool to stimulate the development of priority sectors of the economy. At the federal level, the most important institutions are Vnesheconombank, the Federal Corporation for SME Development, the Industrial Development Fund, the Single-Industry Towns Development Fund, the Far East Development Fund, the Russian Export Center. They provide support to small and medium-sized businesses by providing consulting, property and financial assistance. Special emphasis is placed on promotion of business projects and their concessional financing. Regional binding of innovative business projects is revealed. Their success depends on the effectiveness of the federal support system, funding from development institutions, the development of innovative infrastructure, the institutional and business environment formed at the level of a particular region, social infrastructure, the availability of qualified personnel, comfortable living conditions. The instruments of support of innovative entrepreneurship in the regions are considered. The system of institutes of business development in Irkutsk region is studied. It is composed of the following organizations: the Business Support Fund of the Irkutsk region; Corporation of Development of the Irkutsk Region; the Industry Development Fund of Irkutsk Region, Agency Of Investment Development of Irkutsk Region; Irkutsk Regional Guarantee Fund; the Microcredit Fund of the Irkutsk Region. The experience of development of institutions to support small and medium-sized businesses in the Irkutsk region is of interest to other regions because it involves comprehensive support for business structures, and also allows for support on terms that banks cannot provide (at a lower interest rate). Prospective federal and regional projects within the framework of the national project ‘Small and medium-sized entrepreneurship and support of individual entrepreneurial initiative’ are considered.