To examine the morphology and motility of the distal small bowel of infants with rotavirus gastroenteritis using non-invasive/non-ionizing imaging technology. Prospective, non-randomized observational study of five infants with symptomatic rotavirus infection. Infants were imaged by real-time magnetic resonance imaging (MRI) and ultrasound within 5 days of onset of gastroenteritis symptoms. Imaging studies were repeated in the convalescent period 5 to 9 weeks later. Three of five infants had a significant increase in the ileal wall thickness visualized by ultrasound during acute rotavirus infection compared with convalescence. The number and size of mesenteric lymph nodes visualized by ultrasound appeared similar in the acute and convalescent phases, as did peristaltic activity assessed by MRI. Abdominal ultrasound can detect changes in ileal wall thickness in infants with rotavirus infection. These changes may reflect ileal inflammation elicited by viral infection. Such studies may prove useful in evaluating morphologic response to attenuated rotavirus vaccines.