Risk management is based on objective knowledge of nature and character, forecasting and assessment of the negative factors that affect the innovation success at times. In the analysis of the innovation activity uncertainty, qualitative risk valuation usage can be performed by rating, for example, on the basis of the ranking with following coordination of expert opinion. When performing the quantitative risk valuation it is possible to use the method of mathematical statistics and the theory of probability to anticipate negative effects and decrease the probability of their occurrence. Quantitative risk valuation is necessary to determine the discount rate, which includes a risk premium. In risk management different methods should be used. Among them - the method of risk diversification, the method of reducing uncertainty through the formation of such a structure of assets that decreases the possible fluctuations in the projects profitability. Also rationing and hedging methods are being used as financial and economic risk management levers in organizations-innovators. Risk insurance should be maintained according to the generally accepted contractual commitments between the insurer and the insurant.