The article discusses the issue of protection of natural persons in the Catholic Church in Poland in connection with the entry into force of the provisions of Regulation of the European Parliament and of the Council on the protection of natural persons with regard to the processing of personal data and on the free movement of such data. On this canvas, the Author deals with the issue related to the determination of relations between Churches and other religious associations and the European Union, seeking an answer to the question whether EU institutions have the competence to issue legal norms in the field of religious law, and thus to determine the status of these organizations.