Objective: To determine the presence of Helicobacter pylori and, if detected, its potential prevalence in causing recurrent aphthous ulcers confined to mucos-aassociated lymphoid tissues of the pharynx. Design: Prospective, controlled clinical trial. Setting: Otolaryngology Department of Tanta University Hospitals, Tanta, Egypt. Patients: A total of 146 patients with recurrent multiple aphthous ulcers of the oral cavity and pharynx and 20 normal control subjects. Interventions: Patients were assigned to group 1 (n = 58), in which the ulcers were strictly limited to the lymphoid tissues, or group 2 (n = 88), in which the ulcers were randomly distributed in the oral cavity and pharynx. Helicobacter pylori DNA was extracted from 3-mm-diameter tissue samples, and polymerase chain reaction amplifications were performed for the 16S ribosomal RNA gene. Main Outcome Measure: Positivity for H pylori. Results: In group 1, 39. patients (67%) were positive for H pylori DNA, while in group 2, 9 patients (10%) were positive (chi(2) test, p < .001). It was not detected in any of the 20 control samples. Conclusion: Our results support a possible causative role for H pylori in recurrent aphthous ulcerations with a characteristic distribution and affinity to mucosa-associated lymphoid tissues of the pharynx.