Genetically modified organisms make an important part of today's world. The ecosystem and its self-regulation have been damaged, i.e. the relationship between input and output elements does not occur on a spontaneous, natural level. In addition, people have realized the importance of eating habits and the quality and safety of the same is being discussed in various areas (legal, economic, political). After regulating national provisions in the area of food safety, it is necessary to define a supra-national framework in order for people to be protected to the fullest extent possible. Therefore, the subject matter of this paper is to study transboundary movement of genetically modified organisms and the analysis of relations between the Member States in the European Union. In the entire process of transboundary movement of genetically modified organisms, it is necessary to harmonize the needs of the exporting country and the importing country. It is imperative to coordinate surveillance of genetically modified organisms with an aim of preserving biodiversity and human health. Regarding legal documents, it is necessary to outline the following documents that regulate this matter: Regulation (EC) No.1946/2003 of the European Parliament and of the Council of 15 July 2003 on transboundary movements of genetically modified organisms, the Cartagena Protocol, Directive 2001/18/ EC of the European Parliament and of the Council of 12 March 2001 on the deliberate release into the environment of genetically modified organisms and the repeal of Council Directive 90/220/ EEC. The methods used in this paper are the following: method of analysis and synthesis, historical and comparative method.