The mandatory monitoring of environmental effects is an important element of the regulatory frameworks for genetically modified organisms (GMO) in the European Union and Switzerland. However the implementation of GMO monitoring at the national and EU-level, specifically for the cultivation of GM plants, proved to be a challenging issue and is subject to ongoing discussions. To provide substantial input the National Environment Agencies in Austria and Switzerland and the Federal Agency for Nature Conservation in Germany jointly outline necessary elements and requirements for an appropriate GMO monitoring in this policy paper. The recommendations are based upon the expertise of the three Agencies as competent authorities or advisory bodies with regard to GMO monitoring and interrelated issues of environmental protection and nature conservation.