The essence and assessment of the innovative potential of the ATU Gagauzia development region is dedicated to identifying the key carriers of the region's overall economic potential: the institutional potential of the autonomy management bodies, the components of economic development potential of the territory, the innovative potential of small and medium-sized enterprises of ATU Gagauzia. In the present situation, an important feature of the innovation potential is the existence of knowledge-generating institutions, the adhesion of the region to international innovation networks, the optimal relationship of territorial and omnipresent knowledge within the region, the existence of spatial networking elements. Thus, the author proposes to define the region's innovative potential as a complex, spatially and dynamically organized system of interconnected and balanced potentials (economic, institutional, research and innovation potential) put in operation by a cooperation mechanism (between science, authorities and the business environment) and have achieved a synergistic effect.