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The aim of this study was to compare different methods of detection of Helicobacter pylori (H. pylori) in the dental plaque of dyspeptic patients. After recording the clinical indices, culture and polymerase chain reaction (PCR) methods were performed on plaque samples, while rapid urease test in addition to these tests was carried on gastric samples from 67 dyspeptic patients who attended for an upper gastrointestinal endoscopy. Forty-seven of 67 patients were H. pylori-positive in gastric biopsy material whereas the microbial dental plaque from 19 patients demonstrated H. pylori positivity detected by PCR. Among the patients, 25.4% harbored H. pylori both in the stomach and in microbial dental plaque. No significant correlations were found among the presence of H. pylori in the stomach, in plaque, and clinical variables (P > 0.05). Although oral hygiene was observed optimal and the mean of pocket depth was not found to be higher, the prevalence of H. pylori was observed to be higher in dental plaque. According to our results, PCR technique gave the highest detection rate both in gastric biopsy and in dental plaque compared to the other methods used.