Small bowel rejection occurs in patches; therefore, to detect bowel rejection in situations where a stomal biopsy appears normal under the light microscope, we studied the ultrastructural changes in bowel microvilli following heterotopic small bowel transplantation in rats. Thin sections of bowel biopsy specimens, which appeared normal under a light microscope, were selected and examined under an electron microscope for microvillous changes. Microvillous changes were seen in both the syngeneic and allogeneic groups on the 2nd and 4th postoperative days, but these changes were absent in the syngeneic group by the 8th postoperative day, although they were still detected in the allogeneic group. Thus, following small bowel transplantation, electron microscopic analysis is recommended to confirm rejection with a patchy distribution after the 8th postoperative day.