In contrast to healthy conditions, intestinal epithelial cells (IECs) stimulate pro-inflammatory CD4⁺ and CD8⁺ T cells during Crohn's disease (CD). The underlying regulatory mechanisms remain unknown. Here we investigated the epithelial expression of MHC I and MHC II and its interference with endocytic pathways, in vivo. During ileoscopy, ovalbumin (OVA) was sprayed onto ileal mucosa of CD patients (ileitis and remission) and controls. The epithelial traffic of OVA and MHC I/II pathways were studied in biopsies using fluorescence and electron microscopy. We found MHC I and MHC II to accumulate within multivesicular late endosomes (MVLE) of IECs. Faint labeling for these molecules was seen in early endosomes and lysosomes. MVLE were entered by OVA 10 minutes after exposure. Exosomes carrying MHC I, MHC II and OVA were detected in intercellular spaces of the epithelium. OVA trafficking and labeling patterns for MHC I and MHC II in IECs showed no differences between CD patients and controls. Independent of inflammatory stimuli, MHC I and MHC II pathways intersect MVLE in IECs which were efficiently targeted by luminal antigens. Similar to MHC II-enriched compartments in professional antigen presenting cells these MVLE might be critically involved in MHC I- and MHC II-related antigen processing in IECs and the source of epithelial released exosomes. The access of luminal antigens to MHC I in MVLE might indicate that the presentation of exogenous antigens by IECs must not be restricted to MHC II, but might also occur as "cross presentation" via MHC I to CD8⁺ T cells.