The intestinal epithelium is a critical interface between the organism and its environment. The cell polarity and structural properties of the enterocytes, limiting the amount of antigen reaching the epithelial surface, form the basis of the integrity of the epithelium. However, apart from their participation in digestive processes, the enterocytes perform more than just a passive barrier function. The resistance of the tight junctions regulates the paracellular transport of antigens. Furthermore, the enterocytes take up and process antigens, involving two functional pathways. In the major pathway, enzymes in the lysosomes degrade the antigens. In the minor direct transcytotic pathway, the antigens are not degraded and are released into the interstitial space. Moreover, the enterocytes can present processed antigens directly to T cells and are often directly involved in immune processes. In inflammatory conditions, the properties of the epithelial barrier and the outcome of the immune response to luminal antigens can be changed.