Abstract: The research subject is the system of safety of innovative activities and products manufactured by small and medium enterprises in the Republic of Bashkortostan. Innovative activities of enterprises of this sector of the economy annually spread in new sectors of science and production. Thus, the topicality of the problem of the harm of innovations increases, and appears the necessity to solve the problem of the safety of innovative projects. The key aspects of the research are defined within the situation analysis characterized by the growing necessity to develop import substitution. The author applies the system approach to the analysis of development of innovations in the Republic of Bashkortostan; within this approach, the author applies the social method of evaluation of the impact of innovations on the main spheres of social life. The author carries out comparative analysis of the structure of small and medium enterprises in the Republic and specifies the terminology. The author offers the measures to improve the safety of innovative activities, particularly: imposition of additional responsibility on those involved in the development and introduction of innovative products and those using innovative products; creation of analytical and diagnostic centers for innovative products’ safety.