The Master’s thesis deals with the area of conducting process audits in a large multinational corporation focused on manufacturing and distribution of medical devices, which has a subsidiary in the Czech Republic. The thesis discusses the analysis of the current set up of the internal audits‘ system in the corporation and there are changes of the quality system being proposed on the basis of the analysis, whose aim is to achieve a full compliance with the requirements of the US administration FDA, the standard ISO 13485 as well as the recent requirements on performing process audits. The emphasis is also put on the setting of the system such that it provides the highest possible added value for its users, can be easily implemented in practice and is flexible as well.