The incidence of Crohn's disease (CD) lesions in the upper gastrointestinal (GI) tract of both adults and children is frequently underestimated. In this prospective study, a total of 31 children suspected of having Crohn's disease were systematically examined to identify upper digestive tract lesions. They all underwent barium transit endoscopy with multiple-level biopsies. Typical clinical symptoms suggestive of upper GI tract involvement were found in 5 children (16%), radiological signs in only one child (3%), endoscopic lesions in 13 children (42%), and specific granulomas in 12 children (39%). In eight of these 12 children, the biopsies were taken from macroscopically normal areas of the esophagogastroduodenal mucosa. One of the 31 children had no abnormal radiological and endoscopic features suggestive of CD on the distal small bowel and the colon. There was no correlation between the clinical, radiological, and histological data. Endoscopy plus biopsy provided a positive diagnosis in 39% of cases and a confirmation of the diagnosis in 87% of cases. Endoscopic and histological evidence of CD of the upper GI tract is often present despite an absence of clinical symptoms or radiological changes. Upper GI tract endoscopy with multiple biopsies may be important in the evaluation of this condition and even in some cases for the establishment of the diagnosis.