Abstract: Intestinal transplantation has become the most ideal treatment for intestinal failure. Modern clinical intestinal transplantation includes three types: isolated intestinal transplantation, combined liver-intestinal transplantation and abdominal multivisceral transplantation. The immunological, anatomical and physiological characteristics of intestinal grafts significantly differ from those of other solid transplant organs. Consequently, intestinal grafts could develop specific and severe complications, such as acute rejection, chronic rejection, graft-versus-host disease (GVHD), infection and posttransplant lymphoproliferative disease (PTLD), among which acute rejection and infection are extremely challenging. Endoscopic examination and intestinal mucosal biopsy of intestinal grafts could be performed to make timely diagnosis and differentiation of these complications, then deliver targeted treatment and guarantee the long-term survival of recipients and intestinal grafts.