The article aims at analyzing the role of cross-border cooperation in the development of innovation potential of the Baltic Sea Region. The author analyzes the projects in the framework of the Neighborhood Programs implemented in 2000—2006 and related to the development of innovation potential in the Baltic Sea Region, particularly in the South-East Baltic. The author makes the conclusion about the need to increase the share of innovative projects with the participation of the regions of North-West of Russia; actors fr om the Nordic countries, wh ere regional cooperation is an important engine for innovation development, should be actively involved in these projects.