The aim of this study is to determine the distribution of histological changes of rejection in small intestinal transplantation. Thirty-nine rats were randomized into two groups: group I (n = 15), syngeneic transplants and group II (n = 24), allogeneic transplants. Grafts were excised and examined on days 2, 4, and 8 after transplantation. All grafts of the syngeneic group showed normal mucosa by day 4. However, by this time, all grafts of the allogeneic group demonstrated rejection changes with a patchy distribution in the mucosa. Therefore, with a biopsy from the stoma site there is a risk of missing early rejection.