The main objective of this paper is to analyse the structural changes in European Agri-food systems in the last 30 years in order to verify the presence of a convergence process towards a more homogeneous structure among EU countries. This analysis considers the relative importance of the main components of Agri-food systems (agriculture, food industry and food consumption) and how they change over time. The analysis of convergence utilise the European National Accounting Data (from the SEC2 Data Base of Eurostat) from 1970 to 2000 for twelve EU countries. We use tests of convergence on cross section data by countries, but also stochastic kernel methodologies to verify the dynamic evolution of groups of countries inside the EU. The results show there are important process of convergence among countries for the variables of the Agri-food system that are more linked to the economic development, such as the importance of agriculture and food consumption in GDP. On the other hand there are divergences on the variables more linked to the openness degree and to the competitiveness of the Agri-food system. The presence of polarisation process among groups of countries contribute to the permanence of long run structural changes among Northern and Southern countries in the EU.