We reviewed the clinical and pathologic finding of 22 resected allografts from 19 of the 83 children who underwent a variety of small intestinal transplant procedures in the years 1990-2000 at the Children's Hospital of Pittsburgh. Resections were compared with prior mucosal biopsies because resections allow for evaluation of the entire bowel thickness, including the feeding vessels, and obviate the problems of limited sampling. Partial resections that were done soon after the transplant, or soon after additional surgery, were for surgical problems such as leaks, adhesions, and volvulus. None had biopsy features suggestive of rejection or infection. Partial resections done late (6 months or more) after transplantation were more likely to be related to allograft immune biology; two had a sclerosing peritonitis that was confined to the allograft, and one had an obstructing carcinoma arising in the allograft mucosa. One patient had a localized stricture, demonstrated to be due to graft vascular disease at partial resection, and this patient went on to have the allograft removed a year later for chronic rejection. Early complete allograft enterectomies were for refractory acute cellular rejection, 1-2 months following transplant. One was removed for pancreatitis and liver failure from operative complications. Late allograft enterectomies were generally for chronic rejection, some with residual acute rejection, but there were also a number of patients who had multiple superimposed conditions such as cytomegalovirus, Epstein-Barr virus, and post-transplant lymphoproliferative disorder in various combinations. One had idiopathic scarring and developed an adynamic bowel that remains unexplained. Examination of the resected specimens allows for dissection of the multiple contributions to graft failure, especially the vascular disease that can rarely be seen on mucosal biopsy. An unexpected finding was the impressive hypertrophy of neural elements, nerves, and ganglion cells in many of the patients, the significance of which requires further investigation.