A few studies have reported increased numbers of mast cells (MC) in intestinal mucosa of patients with Crohn’s disease (CD). Also, several studies have established that eosinophils are increased in colonic mucosa of adults; however, the distribution of MC and eosinophils in gastroduodenal mucosa of children or adults with CD is not established. Interestingly, MC and eosinophils in gastroduodenal mucosa have been shown to play a role in abdominal pain of functional dyspepsia. We conducted this pilot study to enumerate MC and eosinophils in mucosa of stomach and duodenum of children with CD.