Tropheryma whipplei has long been considered as a rare bacterium causing a rare disease, Whipple's disease. However, recent advances now suggest that T. whipplei is a ubiquitous environmental bacterium that may cause gastroenteritis, commonly associated with viral pathogens. We developed an animal model to support this hypothesis. We found that orally given T. whipplei induced diarrhea in mice, without spreading into the intestines. Aggravating factors, such as damage to the intestinal mucosa, favored bacterial spreading. Indeed, bacterial presence was prolonged in stools of dextran sulfate-treated mice, and bacteria were detected in the colon. This resulted in an immune response, with T. whipplei-specific serum IgM and IgG and fecal IgA, as measured by newly introduced immuno-polymerase chain reaction technique. Our results confirm that T. whipplei is an agent causing gastroenteritis and suggest that existing mucosal damage may favor bacterial invasion of tissues.