Introduction. The process of interaction of economic subjects of the national innovative system proceeds in the conditions of uncertainty at any level. Risks therefore exist. Risk identification and competent risk management are necessary to ensure the stability of economic subjects themselves and the whole system formed as a result of the interaction among these subjects. Theoretical analysis. On the basis of generalization of the existing theoretical researches on the problem of economic risks, the paper differentiates such concepts as risk and uncertainty, systematizes economic risks, and provides the author’s treatment of the “risk of interaction” category. Discussion. The result of the research conducted is identification of most topical and significant (for the modern economy) risks of interaction among main actors of the national innovative system (science, business, and the state). Among which, the development rate loss risk of an economic subject, the risk of economic losses as a lost profit and a half-received income, the risk of unclaimed training courses, the risk of increased budgeted expenses, low rates of the economic growth, and the risk of loss of the stability of a system.