BACKGROUND Helicobacter pylori (H. pylori) infection is the most common chronic bacterial infection in humans. Its prevalence in Omani adults and children is not known. OBJECTIVE To report histology-based H. pylori infection prevalence in Omani children. METHODS A retrospective study of biopsy proven H. pylori infection in children over a 3 year period in a single center. Age, gender, indication for endoscopy, history of recurrent abdominal pain, and anemia were compared between H. pylori-positive and negative children. RESULTS Of 143 patients who underwent endoscopy, gastric biopsies were available on 112. The overall prevalence of biopsy proven H. pylori infection was 25%. The prevalence in children with recurrent abdominal pain was 30% compared to 22% in children who underwent endoscopy for other indications (p = .382). The prevalence increased from 7% in children aged <5 years, to 33% in those aged between 5 and 10 years (p = .010). There was no significant difference in the prevalence between the 5-10 years age group (33%) and older age group (29%) (p = .814). There was no significant difference in gender or anemia between the two groups. CONCLUSIONS This study represents the first reported study on the prevalence of biopsy proven H. pylori infection in Omani children. H. pylori infection prevalence is 25%, is lower than regional and many Arab countries. The prevalence appears to increase till age of 5 years. There was no significant association between H. pylori and recurrent abdominal pain, gender, or anemia.