Major histocompatibility complex (MHC) class II expression by intestinal epithelial cells (IECs) has been described in inflammatory bowel disease patients. However, the role of epithelial antigen presentation in the maintenance of immune homeostasis remains unclear. We determined that colonic IECs possess important features of antigen presenting cells, as they express MHC class II in response to IFNg signalling, are able to take up and to process antigen and express the co-inhibitory molecule programmed death-ligand 1. Using targeted deletion of MHC class II expression in IECs, we demonstrated that colonic IEC antigen presentation plays a minor role in controlling colonic inflammation but might be important in facilitating the resolution of chronic inflammation. Small intestinal IECs express MHC class II at steady state and loss of epithelial antigen presentation at this tissue site resulted in the near loss of CD8aa+ CD4+ IELs. However, the functional consequences of this loss remain to be determined. In addition, we investigated the role of epithelial antigen presentation in modulating regulatory T cell responses and demonstrated that loss of caecal IEC MHC class II expression resulted in increased FoxP3 expression and IL-10 production by H. hepaticus-specific CD4 T cells in H. hepaticus colonised mice during intestinal inflammation. An experimental repeat, characterised by lower caecal IEC MHC class II expression, did not show these CD4 T cell changes, highlighting the importance of the tissue microenvironment in supporting antigenspecific CD4 T cell responses by IECs. To further dissect the importance of epithelial antigen presentation, in vitro colonic organoid and H. hepaticus-specific CD4 T cell co-cultures were established. This co-culture system revealed that IECs activate microbe-specific CD4 T cells in an antigen specific manner and modulate their effector phenotypes and functions. These results show, that IECs can function as non-conventional antigen presenting cells but the functional consequences of epithelial antigen presentation in vivo require further investigations.