The article deals with the development and implementation of innovative development programs as an ordered sequence of decisionmaking. Innovations are considered as a specific form of chaos or disorder in the transition to a new level of development. As known, innovative projects have a high level of internal and external uncertainties. Therefore they are difficult for evaluated using classical mathematical methods. In this case authors proposed to use fuzzy entropy for the selection of innovative projects. It can successfully act as important mathematically justified criteria permitting controversial selection of the projects. The paper presents definition of fuzzy entropy and corresponding formulation of the problem. Numerical example of fuzzy entropy calculation under conditions of uncertainty has been given. Then also has been developed fuzzy approach for evaluating the risk of innovative projects in the conditions of uncertainty. Presents the general formulation of the problem, describes the ways of it solutions, presented graphical interpretation and analyzed the results. Thus, for evaluating risks of investment projects can be used the apparatus of fuzzy sets which takes into account the non-recurring conditions and a high level of uncertainty in their implementation. Considered approach allows select projects eligible for inclusion in innovative development program. This selection taking into account the regional innovation potential, the presence of uncertainties with the different nature of the occurrence. JEL classification:C02; O31