The aim of the research was to reveal main problems associated with the use of state programs funding mechanisms
for basic research in health (medical) sciences in Russia, as main instruments of state policy.
The source of information were �State Academies of Sciences Program of basic investigations for the period of 2013�2020
years� and other normative and legal acts in the sphere of planning and public financing of science and research. A study
completed by using documentary, analytical methods, as well as methods of descriptive statistics and expert estimates.
In analyzing financing from the federal budget for scientific research for civilian use within government programs
calculations section, subsection of the budget classification, reflecting expenditure on scientific research (0110, 0112,
0208, 0313, 0403, 0411, 0504, 0604, 0708, 0803, 0908, 1005, 1104, 1203).
Feature of the current situation is in an indeterminate state basic science after the liquidation of the Russian Academy
of Sciences as a structure that generates through subordinate organizations the bulk of new knowledge and innovation
in the country. Reform of the Russian Academy of Sciences led to the destruction of a coherent system of relations
in science, to the Federal agency of scientific organizations for management of resources, Ministry of Education and
Science and Russian academy of Sciences. Strict rationality and bureaucracy was extremely negatively perceived in
academic science. The analysis of the subject structure of the medical unit actualized in 2015 of the Program of basic
research of the state academies of sciences for the period of 2013�2020 showed that the distribution of the federal
budget for basic research are not consistent with the priorities in the health sector, it does not account for changes in
departmental affiliation Organizations of Medical Sciences.
The authors prove the necessity of functional and managerial integration of academic medical institutions in the
unified system of scientific research, creation and implementation of medical innovations into practical health care.