In this article presents a theoretical overview of the concepts of innovation systems at the regional level. Investigated factors preventing implementation of innovations, as well as leading to increased innovation activities of enterprises. Listed conclusions concerning the regional disproportions in the innovative development of the Republic of Moldova. Analyzed the difficulties faced by peripheral regions in the development of dynamic innovation systems. Peripheral status of the region should be eliminated the active role of the existing actors of innovation based on building interactive innovation networks, actingas a conductorof innovative processes in the local economy and accelerate its integration into the global economy.