In modern conditions of management and strict state regulation of pharmaceutical activity, the problem of using the internal audit system in the organizations of the pharmaceutical market is acute. In addition to the system of state control, independent control — external and internal audit — became widespread. In these conditions, taking into account the peculiarities of pharmacy organizations, it became necessary to develop organizational principles and methodological approaches to the implementation of internal audit of pharmacy organizations.?This study develops the theory of internal audit in pharmacy organizations. It allows on the basis of a documentary study of the regulatory aspect in the field of internal audit of pharmacy activities to substantiate organizational and methodological approaches to optimizing the conduct of internal audit. The article sets forth the basic principles of internal audit taking into account classification features that can improve the management of a pharmacy organization. The basic principles of the internal audit of pharmacy organizations can be divided into professional and ethical. In the course of the study, we added the following principles of the internal audit of a pharmacy organization to the list of ethical principles and professional principles of auditors, which can serve as an example in the development of local documents for internal audit in any organization: appropriateness, principle of practical benefit, consistency, logical harmony - to ensure clarity of wording, integrity and clarity of presentation, orientation on the interests of owners (the auditor should understand that he protects the interests of owners from internal economic violations).