The paper discusses the evolution and current forms of agreements between federal, regional and municipal governments, as well as between the constituent units of the Russian Federation and municipalities. It analyses the problems and prospects of using these regulatory instruments. The purposes of this paper are to examine the current context of making intergovernmental agreements in Russia, to provide a comprehensive vision of contemporary state of this instrument of shaping intergovernmental relations, and to assess the prospects for their further practical use in the Russian Federation.