The usefulness of isolated intestinal pouches of an intestinal allograft for monitoring mucosal histology during rejection episodes was studied in a canine model. Total small intestinal autotransplantation was performed in four dogs, and allotransplantation in 18 dogs. Isolated pouches from the proximal and distal ends of the allografts were brought to the skin as stomas. Serial biopsies were obtained from these pouches. Nine allotransplants were treated with a suboptimal dose of cyclosporine. Nine allografted dogs were not immunosuppressed. Biopsies from all animals were normal the first two days postoperatively, and remained so in the autotransplants. Mononuclear cell infiltration in the lamina propria and submucosa was seen up to five days before death from rejection of the allograft in dogs on cyclosporine. At autopsy, all dogs had histologic findings in the transplanted bowel similar to those of simultaneously obtained pouch biopsies. The results show that histologic changes in isolated pouches from intestinal allotransplants reflect changes in the incontinuity segment of the graft and, therefore, such pouches can be used for histologic monitoring of the graft.