The article describes the procedures for identification of the main problem, structuring and analyzing of problems of an organizational system in order to create an information base of the process of forming alternative managerial decisions. This base is a prerequisite for the selection of an optimal management solution aimed at solving the problem that arose under the influence of disturbing factors of the external and internal environment of the functioning of the organizational system and cause a violation of its equilibrium status. To identify the main problem of the organizational system, monitoring of its status is built, which includes the following stages: formation of the objective and an information base; analysis and evaluation of the current status of the organizational system; situational analysis of the problem development; diagnostics of the status of the organizational system at the end of the specified period; report on the monitoring results. To structure the problems, the «problem matrix» method is used in conjunction with the plotting of the problem-oriented graph. Possible methods of analysis of the generated problems are characterized.