Abstract: The study concerns, the problems of strengthening the currency of intellectual potential against the backdrop of a crisis. The researchers have revealed the role of the brain capital in the system of new economic relations of innovation production, analyzed the impact of the institutional changes on the development of economic relations. A special attention is paid to the fact that under present-day conditions the health level, qualification, skill to apply knowledge, competence are the basic elements that form new economic relations of innovation production. On the data basis of the concept of long-term socio-economic development of the Russian Federation for a period till the year 2020, it is stated that Russia falls behind the level of economic development of other countries in spite of its possessing high educational potential. It is explained by inefficient use of actual intellectual potential and irrational carrying out investment in it. On the basis of the research to be conducted, the researchers suggest creating an innovative system with the following subdivisions: research center↔enterprise-customer↔state. The main advantage of the new model of innovative system is openness to dialogues and communication and possibility of self-organization. The research is based on the wide use of methods of analysis and synthesis, systemacy and complexity, comparative analyses, factor analysis and the methods of structural-functional, statistic and retrospective analyses. It has been reflected comparative characteristic of the notion “brain capital” of an organization, singled out the scheme of system generating of the intellectual capital of the organization, proposed the measures of the problem solving of the development of organization intellectual capital. It allows the authors to substantiate the thesis about the necessity of all-round macro- and microeconomic policy oriented to the strengthening of the role of the brain capital in the development of organizations and the country on the whole. The main results of the research have been reported and discussed at the theoretical and practical conferences of the international, all-Russian, regional levels. Methodological theses of the research are used by the researchers in the educational processes in disciplines lecturing. Formulated by analysis results recommendations for effective functioning of the brain capital of organizations have high practical significance. The practical importance consists in the possibility of the use of abstract theorem and practical recommendations stated in the research work by the bodies of legislative and executive power in their developing and realizing the federal and regional anti-crisis programmes. Conclusions, obtained in the processes of exposure of a role of intellectual capital of organizations against the backdrop of a crisis can be used by: organizations for innovation development; a high school in lecturing courses on institutional economics, microeconomics, innovation management.