Background: Otitis media with effusion (OME) is a common disease in children. Viral or bacterial infections, allergy, adenoids, functional abnormalities of the Eustachian tube, and gastroesophageal reflux might have a possible role in the pathogenesis of OME. However, the exact pathogenesis of OME is still unsettled. Objectives: The purpose of this study was to compare Helicobacter pylori prevalence rates in the nasopharynx of pediatric patients with and without OME. Patients and Methods: Eighty-four patients (50 males and 34 females) who were subjected to adenoidectomy and myringotomy were included in the study group. Ninety-one patients (48 males and 43 females) who had only adenoidectomy were selected as the control group. Detection of H. pylori was done by polymerase chain reaction (PCR). Results: Adenoid samples were positive for H. pylori in 21 (25%) patients in study group and 18 (19.8%) patients in control group. In the study group, 36 (42.8%) effusion samples (otitis media) of the patients were positive for H. pylori. In an analysis that compared H. pylori-negative and -positive children, the odds ratio (OR) for the occurrence of H. pylori was 1.35 (95% CI, 0.66 - 2.71). The association of age with H. pylori positivity decreased for 1-5 years age group, (1.09; 95% CI, 0.39 - 3.05) but increased for the 6-10 years group (OR, 1.48; 95% CI, 0.61-3.58). Furthermore, the association of sex with H. pylori positivity decreased for the male group (OR, 1.21; 95% CI, 0.50 - 2.91), but increased in the female group (OR, 1.44; 95% CI, 0.51-0.4.05). Conclusions: Heavy colonization of H. pylori in adenoid tissue and middle ear might have a role in pathogenesis of this infection. For OME cases resistant to medical treatment, it might be meaningful to evaluate the patient for H. pylori.