In the first place, it will negatively affect the small innovative companies with share of payroll in the total budget up to 80% and less impact on the enterprise of the commodity sector, where the share of wages does not exceed 3%. Thus, we can say with certainty that in 2009 the tendency for reduce innovation-oriented enterprises. In August 2009, entered into force on the federal law authorizing Budgetary scientific organizations and higher education institutions to create commercial organization. In this case, exclusive intellectual property right is assigned to university. However, in order that this law has begun to function effectively, requires the adoption of a number of changes to the bylaws that would allow Higher education institutions to dispose of the profits from the activities of innovative enterprises, to contribute to the charter capital of economic entities, not only intellectual property rights, but also physical assets. Fund to support small enterprises in the scientific-technical sphere (Bortnik Fund) has decided to launch in 2010, a new program – START-science, which, in essence, aims at providing financial support for small innovative enterprises, created with the participation of universities. Currently, active work is underway to prepare the base of the bill on the foundations of innovation system of Russia, which will fix the basic concepts in the field of innovation and provide legal grounds for granting exemptions to small innovative enterprises. Concern is the weak interest of private business to invest in science and innovation, the main source of funding which is the federal budget.