Microsatellite instability (MSI) is a hallmark of carcinomas occurring in the setting of hereditary nonpolyposis colorectal cancer, but can also be found in sporadic and colitis-associated tumors. The incidence of MSI in Crohn's disease is unknown and has usually been reported in the colon. We report the case of a 26-year-old man, diagnosed 4 years earlier with Crohn's disease, who developed an associated small bowel adenocarcinoma. The tumor was found to have high levels of MSI by immunohistochemical staining and by MSI testing. No mutations were identified by genetic testing, and high levels of MSI are most probably due to hypermethylation.