The yield of several commodity crops is provided in large part by genetically modified crops in North and South America. However, reservations exist in Europe due to possible negative effects on human health or environment. This paper aims to analyse the current research priorities identified in EU countries and to engage European stakeholders into the formulation of future common research needs regarding the effects of the possible adoption of commercially available and forthcoming genetically modified organisms (GMOs) in the areas of socio-economics, human and animal health, and environment. Additionally, it aims to identify the requirements for sharing available research capacities and existing infrastructures. First a mapping exercise of existing research activities in Europe was performed. A questionnaire was developed on a web-based platform and submitted to national focal points to collect information from EU Member States. Information was collected from 320 research projects conducted in the last 10 years in Europe. To refine results of the surveys, twenty invited experts and stakeholders from the public funding agencies of different EU Member States participated in an international workshop. This paper reports the main findings of these activities.