The aim of this paper is to examine the relationship between the factor endowment and the pattern of intra-industry trade. Our empirical analysis relates to Hungary’s intra-industry trade in agri-food products with 26 member states of the EU over the period 1999-2010. Estimations reject the comparative advantage explanation of vertical intra-industry trade and provide partial support the prediction of Flam and Helpman model. Findings highlight that nature of factor endowments play also important role in explanation of vertical intra-industry trade. Other variables like market size and distance confirm the theoretical expectations. In addition, trade with new member states positively, whilst the EU accession ambigouosly influence the share of vertical IIT.