Purpose: Gastroesophageal reflux (GER) is one of the most frequent clinical disorders affecting the gastrointestinal tract of infants and children and chronic abdominal pain is one of the hallmarks of this disease. The purpose of this study was to find the prevalence of GER in children with chronic abdominal pain that needed esophagogastroduodenoscopy (EGD) for final diagnosis. Methods: All children aged 2–15 years old suffering from chronic abdominal pain that underwent EGD by the author in the only pediatrics gastroenterology ward in south-western of Iran were reviewed and enrolled in this study. The data obtained from the patients files which are kept in the hospital's archive. Results: During 9 years(1998–2007) totally 1156 patients (599 boys, 557 girls) aged 1.5 months to 15 years with different upper GI tract problems underwent EGD in the gastrointestinal ward of Aboozar Children's Hospital, Jundishapour University of Medical Sciences. There were 804 (69.5%) patients (416 boys, 388 girls) older than 2 years who enrolled in our study. Among this age group, we found 449 cases (239 boys, 210 girls) with chronic abdominal pain needed EGD. When the procedure was performed, the diagnosis of esophagitis due to GER was suspected in 86(19%) patients (49 boy-37 girl) by observing obliteration of the Z- line and was confirmed by histopathological changes in esophageal biopsies. There were 8 cases with Barrett's esophagus all aged more than 6 years with history of suspicious symptoms of GERin infancy and later on. Treatment with prokinetic drugs and PPI or H2 receptor blockers was undertaken. Successful treatment was observed in 96% of all patients 6 months after treatment was initiated and on follow up. Surgical antireflux procedure was performed to patients with no resolution of symptoms after 6 months of therapy. Conclusion: In conclusion, GER in children with chronic abdominal pain beyond infancy is not rare ant tends to be chronic and severe and such patients are at high risk of developing serious complications without early diagnosis and treatment.