Development of innovative entrepreneurship in the Russian Federation is particularly relevant at the moment. At the level of the constituents of the Russian Federation were formed their legal frameworks, which should be the rules of relations in the "state - the business community". A program to support small innovative entrepreneurship in universities and research organizations was developed. However, if we turn to official Russian statistics, the regions have a sharp contrast from each other based on the results of innovative entrepreneurship. Thus, for example, possible to isolate whole regions where under the existing regulatory framework, entrepreneurs do not strive to implement innovative projects or invest of ones. This problem and determine the relevance of the study. The study was conducted on the basis of the expert survey of entrepreneurs of Innovation business. Information was collected on the basis of the expert survey, in which respondents were offered questions regarding the structure of uncertainties. There were presented of their description: handling, time of occurrence and existence of nature (in the external and internal environment), predictability and control. Furthermore, as additional conditions to determine the uncertainties and their impact on innovative entrepreneurship are defined as follows: the causes that give rise to uncertainties in the sources of information used by entrepreneurs in decision-making, the role of government in the development of innovative entrepreneurship institute, the structure of relations between the agents, appraisal systems support entrepreneurs and authorities types of assistance that obtained by ones. The sample size was 6700 expert survey respondents of small, medium, large and very large businesses of Russia. In examining the problem of uncertainties and their impact on innovative entrepreneurship tested the following hypotheses: 1. Causes of existence and uncertainties are determined by Russian regional peculiarities. 2. Among the uncertainties in each federal district there are those arising solely under the influence relations with the bodies of executive power of the Federal Districts of Russia. The result is obtained "points of contact" which allow building harmonious relations in the system "state - business community" and followed by uncertainty avoidance too. Research study financed from Russian Foundation for Basic Research in the year 20142015 as research project No. 14-06-00051 "The implementation of innovative projects and processes under conditions of uncertainty".