A total of 40 children was recruited to assess the role of Helicobacter pylori infection in children with recurrent abdominal pain syndrome. Among 40 children, seven (17.5%) cases were confirmed to have H. pylori infection. All H. pylori-positive patients had active chronic gastritis histologic findings (p < 0.0001); however, the majority of the H. pylori-negative patients had minimal to mild gastritis histologic findings (p = 0.001). Grossly, chronic gastritis picture was present in all children infected with H. pylori and antral nodular gastropathy present in 43%. 71% of H. pylori-positive patients had elevated anti-H. pylori IgG titer; however, 15% in H. pylori-negative patients (p = 0.006). Serum H. pylori assay had a sensitivity of 71% and specificity of 85%; however, sensitivity and specificity of rapid urease test were 86% and 100% respectively. Antral nodularity is a specific, peculiar endoscopic finding of children infected with H. pylori (p = 0.004). Although the present study suggests that H. pylori-related chronic gastritis may play an etiological role in a subgroup of children with RAP syndrome, but the routine screening of H. pylori infection in children with RAP is not recommended, since no compelling data support the significant association between H. pylori infection and RAP syndrome.