This paper reviews the ability and willingness of regions and municipalities to upgrade spatial development using a systemic approach to the selection of program-project priorities and institutions of market development. The potential of individual factors and institutions in the areas of systemic modernization of regions and territories is reviewed; the need for program-project upgrade of the federal structure of the Russian Federation is substantiated. New institutions of regional development - self-development of the regions and municipalities, the formation of business area, program-project planning, spatial development etc. are proposed.