Background:Occasionally, bacteria or viruses enter the tonsils and these organs become overwhelmed by bacterial or viral infection leading to inflammation. Some studies confirmed the presence of Helicobacter pylori in tonsillar specimens of patients suffering from chronic tonsillitis and some others did not. The difference in results in various studies might be due to different laboratory methods. The aim of this study was to investigate the presence of H. pylori Deoxynucleic acid (DNA) in archival tonsillar tissues of patients with chronic tonsillitis by a rapid, sensitive, and specific technique of Scorpion real-time polymerase chain reaction (PCR).Materials and Methods:Scorpion real-time PCR and modified McMullen's staining was performed on 103 archival paraffin-embedded tonsillar samples collected from patients with chronic tonsillitis following tonsillectomy operation.Results:Our findings showed that H Cell and Molecular Research Center. pylori DNA was present in 21.35% of total specimens by using Scorpion real-time PCR. Modified McMullen's staining of paraffin-embedded sections was positive in 19 patients. Out of our 103 samples, 50 samples showed positive a rapid urease test whereas 53 samples demonstrated negative results, 20 produced positive PCR results, and 83 were negative for H. pylori. There was no significant relationship between the presence of H. pylori, sex, age, and place of residence.Conclusion:Although the existence of H. pylori in tonsillar tissue samples of patients with chronic tonsillitis is controversial, however, our results showed that in our studied specimens, a significant number of patients with chronic tonsillitis had H. pylori colonization.