The recent food security crisis has shed light on the importance of agricultural development in the South Mediterranean countries. An ‘urban bias’ and ‘trade liberalisation’ policies have resulted in growing dependence on imports, narrow specialisations and unsustainable production practices. The Euro-Mediterranean integration process has put trade liberalisation in the centre of attention, while the progress in agriculture has been limited. The purpose of this paper is to analyse the challenges faced by agro-food systems in Southern and Eastern Mediterranean Countries, with specific attention to the role of the Euro-Mediterranean integration and the reform of the Common Agricultural Policy. The paper also reviews relevant economic and environmental data in selected South and East Mediterranean countries.