Since the reform of the EU Common Fisheries Policy in 2002, effort has been devoted to addressing the governance, scientific, social and economic issues required to introduce an ecosystem approach to European marine fisheries. Fisheries management needs to support the ‘three pillars of sustainability’ (ecological, social and economic. Fisheries Ecosystem Plans (FEPs) were developed to further the ecosystem approach in fisheries management and as a tool to assist managers consider the ecological, social and economic implications of their decisions. The FP5-funded European Fisheries Ecosystem Plan (EFEP) project developed a FEP for European waters, using the North Sea as a case study. The core concept of the Making the European Fisheries Ecosystem Plan Operational (MEFEPO) project is the delivery of an operational framework for three regional seas. This is the necessary next step in the process. Furthermore, MEFEPO will, based on the lessons learned consider how FEPs can be made operational and developed for other regional areas. MEFEPO will focus on how best to make current institutional frameworks responsive to an ecosystem approach to fisheries management at regional and pan-European levels in accordance with the principles of good governance. This will involve developing new linkages and means of allowing dialogue between the disparate groups of stakeholders, the integration of the considerable body of ecological, fisheries, social and economic research which has been developed in recent years and investigate how existing institutional frameworks need to evolve to incorporate this information and develop both dialogue between the disparate groups of marine stakeholders and develop a decision-making process which integrates a wide breadth of interests. The three areas used by MEFEPO will be the North Sea RAC, North-western Waters RAC and South-western Waters RAC areas.