The immunological problems of small bowel transplantation have not yet been overcome. Frequent severe rejection episodes are common in clinical practice, and GVHD may emerge as a significant complication once rejection is more effectively controlled. Both are caused by the large number of lymphocytes in the graft. There is extensive exchange migration of lymphocytes between graft and host even in the absence of rejection, and persisting donor cells in the host may carry the propensity for GVHD. Various techniques including analysis of host peripheral blood samples are being developed to enable earlier and easier diagnosis of rejection, which should facilitate early treatment and reduce infective complications. The balance between rejection and GVHD can be manipulated experimentally, and clinical trials are under way to determine whether such techniques can improve the outcome for human transplant recipients.