The methodical tools of organization the control over the activities of materially responsible persons in scientific institutions are researched. The functioning of the Institute of Food Resources of the National Academy of Sciences of Ukraine as a co-founder of the Educational, Scientific and Production Complex of "All-Ukrainian Scientific and Educational Consortium" is considered. It is determined that the institute is the leading agency on scientific ensuring of technical and technological progress of food processing industry of Ukraine. The methodical recommendations for organizing the internal control of budget funds managers in their institutions and subordinated budget institutions are considered. It is defined that the basis for the internal control is the responsibility of the manager for control and development of the institution in general. His main tasks are planning and organization of activities; formation of an adequate internal control structure; supervision of implementation of internal control and risk management to make sure that the goal and objectives of the institution are achieved and decisions, including financial ones, will be executed taking into account the principles of legality economy, efficiency, effectiveness and transparency. The concept of the term "responsibility" is considered and the different types of legal responsibility are described. Legal responsibility should be understood as the duty of a person to undergo certain restrictions of state power, provided by law, for the committed offense. The essence of the legal responsibility is as follows: a person, who hasn't executed the responsibility imposed on his/her by law, the new duty is assigned to certain restrictions, negative personal or property consequences. The scientific approaches to the interpretation of the term "material responsibility" are investigated. It is established that the material responsibility can be imposed on any employee who has entered into an employment contract with the owner or the authorized owner of the body. The implementation of labor activities under the civil law contracts is not covered by the sphere of the labor law. Therefore, persons who perform work on the basis of the civil law agreements (for example, under a contract), are responsible for property under the norms of the civil law. The types of material responsibility such as: limited, full, collective (brigade) and increased are considered. The list of grounds for bringing the employee to material responsibility (the presence of the direct harm, violation of the employee or owner of labor duties, causal link between violation and harm, the employee's fault) is studied. The procedure of signing the contract on full material responsibility and indemnity are investigated. The essence of the control over the activities of materially responsible persons is defined. It should be understood as the whole process, which is carried out by the management and employees of the institution, which directed to revealing of deviations and deficiencies in the work of materially responsible persons and bringing the perpetrators to responsibility. The basic directions of improvement of the control over the activity of materially responsible persons in scientific institutions are determined. These can be: the implementation in the institution of the materially responsible people’s instruction, regarding their rights and duties and determining these positions in the job descriptions; the implementation in the institution of the analytical information, where to record the information about the guilty persons, the reasons for the deviations, actions or inactivity of the persons that led to deviations; the formation of a separate subdivision of internal control, which will perform control functions including control over materially responsible persons, or introduction of the position of the internal controller; the computerization of the audit of goods, which will solve such problems as: observance of objectivity, accuracy of results, timing, reduction of labor costs; the development and implementation of a system of internal regulation of the control of the scientific institution, where it is necessary to provide general control questions at the level of the institution, the clearer provisions of internal control which are connected with concrete subjects of its realization, the definition of the rights and duties of persons connected with control activity.