Although research of intra-industry trade (IIT) has been intensive in the last several decades, the empirical literature focusing on this phenomenon in the Western Balkans countries remains limited, especially in agricultural sector. Aiming to contribute to the existing literature, the paper analyses patterns and country-specific determinants of IIT in agri-food products between Bosnia and Herzegovina (BiH) and the European Union (EU) during the period of their mutual trade liberalisation (2008-2018). The analysis employs Grubel-Lloyd indices and Greenaway-Hine-Milner methodology for measurement of IIT, and applies an econometric panel data model using a Poisson Pseudo-maximum likelihood approach in order to estimate effects of IIT determinants. The findings suggest that intra-industry agri-food trade of BiH with the EU is of low intensity and mainly of vertical nature, viewed totally and bilaterally. We found significant positive effects of trading countries’ sizes, common border and history on IIT, and negative effects of the geographic distance and differences in agricultural productivity.