International trade theory suggests that advanced trade integration may lead to higher levels of intra-industry trade (IIT). The enlargement of the European Union (EU) during last decade is as a good example for which to analyse the IIT in agri-food products. The aim of the paper is to analyse the pattern and drivers of horizontal IIT within the EU between 1999 and 2010. Previous empirical studies fail to provide an exact link between the theory and the data. Thus, a new empirical strategy developed to test the predictions of Helpman and Krugman (1985) model is employed. At the country level, Belgium, France, Netherlands and Germany report the highest levels of IIT within the EU. The calculations mainly support Cieslik’s (2005) proposal to find the missing link between empirics and theory of IIT. In addition, the results are robust to alternative subsamples.