Abstract Background: Current diagnostic methods for detecting Helicobacter pylori infection include rapid urease test (RUT), urea breath test (UBT), histology, culture, and polymerase chain reaction (PCR). RUT is the most commonly method to diagnose Helicobacter pylori infection because of its simple, rapid and accurate characters. The aim of this study is evaluation of rapid urease test compared with PCR for diagnosis of Helicobacter pylori. Material and Methods: In this study 94 patients with dyspeptic symptoms attending the endoscopy suite of gastroenterology section of the Firouzgar University Hospital, Tehran, Iran, were enrolled. Patient’s antrum biopsy specimens were collected at endoscopy for the rapid urease test and PCR. Data was recorded on a data sheet and analyzed using SPSS version 19.0. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of RUT was compared against PCR. The gold standard test for the diagnosis of Helicobacter pylori infection was PCR. Results: Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of RUT respectively were 97.2%, 89.2%, 81.4% and 98%. Conclusion: RUT has high sensitivity and specificity for detection of Helicobacter pylori infection.