Helicobacter pylori infection can be a risk factor for non-cardia gastric cancer. In the present study, we aimed to assess the rate of Helicobacter pylori infection, its virulence factor and precancerous lesion among over 50 years old, dyspeptic patients with normal endoscopy. A total of 620 patients over 50 years of age with dyspepsia that referred to Shahid Sadoughi Hospital, Yazd, Iran from December 2018 to January 2019 were evaluated. One hundred fifty patients with normal appearance endoscopy were selected, and six gastric biopsy specimens were taken from each subject. Data were analyzed using chi-square and logistic regression tests. A total of 150 patients with mean age of 65.8±11.9 years old participated in this study. Sixty-three (42%) patients were males. Thirty-four (22.6%) patients had precancerous lesions. Ninety (60%) patients had positive PCR results for H. pylori. H. pylori infection test was positive in 24 (70.6%) patients with precancerous lesion. Sixty-six (57%) patients without the precancerous lesions (116 cases) were positive for H. pylori. There was no a significant difference in the rate of H. pylori infection and its genotype distribution was between patients with and without the precancerous lesions.