The subject of the research is the organization of cooperation between integration interregional associations - parliamentary associations and economic interaction associations of the subjects of the Russian Federation in federal districts during 2005-2012. The issues of forming a cooperation system for economic associations and parliamentary associations are considered, which was determined by the need to create unified rules for integration policy for federal districts and a unified system for coordinating the parameters of strategies and programs for the socio-economic development of the subjects of the Federation and federal districts. The main control functions for the implementation of integration policy in federal districts were carried out by the authorized representatives of the president, with the Councils under authorized representatives being the key coordinating bodies. Attention is drawn to the specific conditions for forming the cooperation system between interregional associations depending on the priorities for the socio-economic development of federal districts. As a methodological basis for the research, historical-genetic, problem-analytical, and historical-comparative methods were used, as well as structural-functional analysis. This allowed for the reconstruction of the historical context of the formation of the cooperation system between interregional associations and the assessment of the effectiveness of their integration potential. The author established that the formation of cooperation between the parliamentary associations of the subjects of the Russian Federation and economic interaction associations in federal districts took place in two stages. In 2005-2007, the basis for the interaction of economic interaction associations and parliamentary associations was the development and implementation of federal target and initiative economic programs. The coordination functions of cooperation for the activities of interregional associations were carried out by the authorized representatives of the president in federal districts, while the control functions were handled by the Ministry of Regional Development. In 2008-2012, with the unification of the main approaches to strategic socio-economic planning, the tasks of coordinating the implementation of socio-economic strategies and programs were handled by the Ministry of Regional Development, while the control functions were transferred to the representatives of the president. Parliamentary associations and economic interaction associations, which directly accumulate practical experience in implementing strategies, are defined as associations solving tasks of an informational-analytical and organizational-technical nature. Overall, from 2005 to 2012, the organization of cooperation between parliamentary associations and economic interaction associations was characterized by managed patterns, and due to the rapidly changing demands of federal policy, it was not fully formed. The implementation of federal agenda tasks was carried out in federal districts on a non-unified basis.