Subject. This article explores the organizational aspects of control activities of universities. Objectives. The article aims to clarify some individual organizational provisions of internal financial control and audit of universities on the basis of a critical assessment of the positions of domestic and foreign researchers, analysis of the current practices of federal institutions of higher education, and the results of the control activities of their founders. Methods. For the study, we used the methods of analysis, grouping, comparison, and generalization. Results. The article clarifies the objectives of the internal financial audit through including in its formulation a provision on the analysis of the quality of financial management of the institution according to the International Standard on Auditing (ISA) 315. It assesses the ways used by universities for internal financial controls and audits, and it analyzes their irregularities in the financial and economic activities. Conclusions. The article concludes that the concepts and organizational frameworks of internal financial control and internal financial audit have not been finalized. Control activities of universities need to be standardized, including the basis of common criteria for choosing the ways of organizing it. The methods used to organize internal financial control and auditing at universities do not comply with the principle of independence.