Pediatric small bowel transplant recipients are susceptible to diarrhea due to rejection or infectious enteritis, particularly of viral etiology. The most common causes of viral enteritis in this setting are rotavirus, adenovirus, cytomegalovirus, and Epstein-Barr virus. This study is the first to compare the histologic findings of rotavirus infection with acute cellular rejection in small bowel transplant biopsies. Three patients with small bowel transplants had rapid stool antigen test-proven rotavirus infection. Endoscopic biopsies during infection were examined, including material from the allograft, native small bowel, stomach, and colon. Biopsies from 2 of the patients during unrelated episodes of mild acute cellular rejection were also evaluated. Blunting of villi was the most common finding in rotavirus infection. Additionally, there was a mononuclear infiltrate that was "top heavy," or denser towards the lumen. There were surface apoptoses but no increase in crypt apoptotic figures. In contrast, during mild acute cellular rejection, there was no villous blunting, the mononuclear infiltrate was diffuse, and there were increased crypt apoptosis. As expected, the changes of acute cellular rejection were confined to the graft, in contrast to rotavirus infection, in which case native bowel often had more pronounced changes. Although the small number of patients limits this study, several histologic features were helpful in identifying rotavirus infection. These were blunting of villi, distribution of the inflammatory infiltrate, number and location of apoptotic bodies, and anatomic location of the effect. A larger follow-up study would be valuable to confirm these findings.