Eradication of Helicobacter pylori, which is associated with diverse gastroduodenal pathologies of varying severity, is sometimes challenging. We conducted a prospective study to determine the effect of tonsillectomy on the eradication of H pylori from the gastrointestinal tract. Our study population was made up of 46 patients-32 females and 14 males, aged 14 to 58 years (mean: 28.84 ± 9.65)-who had chronic tonsillitis and concomitant dyspepsia. An initial gastrointestinal endoscopy was performed to obtain specimens for histology and a rapid urease test. These gastroscopies revealed that 32 patients were H pylori-positive (69.6%) and 14 were H pylori-negative (30.4%); these groups were designated A and B, respectively. The 32 H pylori-positive patients were divided into three subgroups based on the sequence in which they underwent drug therapy and tonsillectomy. All 3 subgroups received the same 14-day combination-drug regimen for eradication of gastric H pylori. The patients in group A1 (n = 12) underwent tonsillectomy prior to receiving drug treatment; 2 months after the cessation of drug therapy, they underwent a second gastroscopy. The patients in group A2 (n = 10) received drug treatment first followed by tonsillectomy; 2 months later, they underwent their second gastroscopy. The patients in group A3 (n = 10) received drug treatment first, then they underwent a second gastroscopy, and then they were taken for tonsillectomy. The success or failure of H pylori eradication was determined by the second gastroscopy. Also, analyses were performed after tonsillectomy to look for H pylori infection in tonsillar specimens. Eradication of gastric H pylori was achieved in 9 of the 12 group A1 patients (75.0%), 8 of the 10 group A2 patients (80.0%), and 7 of the 10 group A3 patients (70.0%); there were no statistically significant differences among the three groups. Likewise, there were no significant differences between any subgroups or combination of subgroups in terms of tonsillar positivity. As far as we know, this is the first study to investigate the effect of tonsillectomy on the outcome of H pylori eradication treatment. In light of our findings, we may speculate that tonsillar tissue does not seem to be a reservoir for H pylori infection. Although tonsillectomy had no significant effect on gastric H pylori eradication in our study, our results might have been skewed by the relatively small size of our sample.