Over a 5-y period, 396 children complaining of recurrent abdominal pain (RAP) underwent upper gastrointestinal endoscopy in order to identify any underlying organic pathology and determine the prevalence of Helicobacter pylori (H. pylori) infection. Histologically confirmed mucosal inflammation was found in 338 out of 396 children (85.4%); in 113 of 396 patients (28.5%), H. pylori was identified on the gastric mucosa. Significant discriminating factors between H. pylori positive and negative children with RAP included age (mean age for positive 11 y vs. 8.1 y for negative, p < 0.01) and gender (male gender predominance in the H. pylori positive, p < 0.001). No significant difference was found between H. pylori positive and negative groups regarding incidence and character of the presenting symptoms. All H. pylori positive children (100%) had abnormal histology compared with 225 out of 283 negative ones (79.5%). Histologically confirmed gastritis was the most prominent finding in H. pylori positive children compared with H. pylori negative (98.2% vs. 19%, p < 0.001). Conversely, oesophagitis was more common in H. pylori negative children (47.7% vs. 27.4%, p < 0.001). The incidence of peptic ulcer was higher in H. pylori infected patients than in the H. pylori negative group (5.3% vs. 1%, p < 0.05). Our data suggest that gastrointestinal pathology is more common than previously thought in children with RAP, while H. pylori infection is a relatively important factor in the etiology of upper gastrointestinal inflammation in RAP syndrome.