Involvement of the upper gastrointestinal tract by inflammatory bowel disease was long held to be a feature of Crohn's disease, whereas ulcerative colitis was considered to be limited to the colon. It is now recognized that ulcerative colitis associated inflammation can involve the upper gastrointestinal tract, primarily the stomach. In addition to aphthoid esophageal ulcers in Crohn's disease, eosinophilic esophagitis and so-called lymphocytic esophagitis occur in association with ulcerative colitis and Crohn's disease. Possible immune mechanisms behind these conditions are presented. The differential diagnosis of inflammation in each site is discussed.