The increasing application of monoclonal antibody technology and FACScan analysis to the phenotyping of immunocytesin situor after isolation from tissues is having a considerable impact on understanding of intestinal mucosal immunity. Cells can be classified as to type and state of activation. So far, however, we have no really acceptable hypothesis for the immunopathogenesis of inflammatory bowel disease. These techniques may need to be applied to clinical situations, such as pouchitis following pelvic ileal pouch operation for ulcerative colitis and recurrence in the neoterminal ileum following ileocolonic resection for Crohn's disease. In these situations, clinical researchers are perhaps defining for the first time the real natural history of ulcerative colitis and Crohn's disease. In the area of autoimmunity and inflammatory bowel disease, the main priority is cloning and identifying putative autoantigens.