Th e article analyses the country and industry specifi c determinants of the horizontal and vertical intra-industry agri-food trade between the Baltic Countries and the European Union in 1999-2013. Results obtained by the GMM panel model estimations suggest that distance is negatively related to IIT, implying that geographical distance is an obstacle for intra-industry agri-food trade. Moreover, factor endowments are ambiguously related to IIT as land is found to be negatively, while labour and machinery to be positively related to both sides of the IIT. Results also show that product diff erentiation fosters two way trade of the quality-diff erentiated goods as a positive relationship exists between the agricultural employment and IIT. As to productivity, all model runs show a negative relationship for HIIT but positive for VIIT, implying that low-quality product exports dominate the agri-food trade of the Baltic Countries. Furthermore, FDI was also found to have a negative relationship with IIT, suggesting that foreign capital does not foster IIT.