Background: The development of endoscopic instruments to evaluate different parts of the gastrointestinal tract improved significantly the information about diseases affecting the gastrointestinal tract, and its management. Methods: The study included 197 children referred for endoscopic examination during the period of October 2002 to September 2005, aged from 3 months to 16 years (average 5.7 years) and 55% of them were males. One hundred thirty two patients (67%) were referred for upper gastrointestinal endoscopy while 65patients (33%) for lower endoscopy.Results: Out of the 30 patients upper endoscopy revealed pale mucosa in 32% and edematous mucosa in 28% of the cases. In 40 % of the cases, no abnormalities could be found. Biopsy examination revealed villous atrophy in 64% and a picture compatible with Crohn's disease in 28%. However, in 8%, no histological abnormality was detected. In patients with unexplained recurrent abdominal pain, UGIE revealed abnormalities in 55% (30% gastritis, 15% duodenitis, and 10% duodenal ulcer). However, in 45% no abnormality could be detected. Histological abnormalities were found in 90% of cases; 45% active gastritis and Helicobacter pylori (HP) organisms in the antral region, 30 % active gastritis without HP and 15% active duodenitis with the HP in the antral region. Collectively, HP organisms were detected in 60% of cases with unexplained RAP. Conclusions: Endoscopic examination can demonstrate definite organic lesions that are necessary for diagnosis. However, a negative endoscopy with normal findings has its role in either reassurance of parents and diagnosis of functional disorders