This article describes the main characteristics of international cooperation in the Baltic Sea Region (BSR) within the framework of the EU macroregional strategy. The analysis of the key directions, structure, and the Strategy implementation mechanisms demonstrates its experimental and innovative nature. At the same time, the authors identify problems and contradictions in the very idea of the Strategy, as well as its actual implementation in intergovernmental relations of the BSR countries. The main factor hampering the Strategy activities is ignoring the key role of Russia the BSR. At the same time, Russia and some non-BSR countries are already members of all significant BSR cooperation instruments. Therefore, there is a need to supplement the EU Strategy for the Baltic Sea Region with the Northern Dimension project. The innovative nature of macroregional cooperation in the Baltic Sea region is manifested in interpreting the region as an indivisible whole rather than an administrative unite serving as a pla tform for various cooperation programmes implemented in its different parts. From this point of view, the Strategy for the Baltic Sea region, apparently inspired by ‘rational functionalism’, can assign a new meaning to the concept of the region.