The small bowel, the largest lymphoid organ in the body and host to a myriad of foreign antigens has presented a formidable challenge for transplantation. In the past 5 years, small bowel transplantation has become a viable clinical entity. Successful transplantation of the small bowel has been achieved as part of multivisceral grafting, combined small bowel and liver grafts and even as isolated small bowel grafts. Allograft rejection remains an important post-transplantation problem, although graft versus host disease has been less of a clinical problem than initially feared. Markers that may serve to predict early rejection have been identified and include: assessment of endoscopic biopsies for enterocyte Class II antigen expression and for mucosal T cell and macrophage infiltration, bowel permeability studies, and measurement of changes in transepithelial potential difference. Earlier detection of rejection and more potent therapy for rejection episodes will be necessary to further improve outcomes.