Several studies showed significant relationships between bacterial counts and the severity and type of disease in patients. The aim of this study was to evaluate the relationship between Helicobacter pylori disease and bacterial count. In this study, 287 patients with dyspeptic symptoms were evaluated. Three variables including patient-reported data, clinical signs and bacterial load of gastric specimens were analyzed. Biopsy samples were collected from patients who were referred for endoscopies because of dyspeptic symptoms. Initially, the clinical status was evaluated and recorded by a questionnaire. DNA extraction was performed and H. pylori was analyzed for bacterial count by Real-time PCR assay and specific primers and probe. The variety range of bacteria in specimens was 10⁴ to 10¹². The results revealed that a greater relationships existed between 10¹² and gastric cancer (p = 0.036), also 10⁴ and acid reflux (p = 0.006) and vomiting (p = 0.047). Real-time PCR assay provides a highly accurate, rapid and precise method for detection of H. pylori and determination of progressive disease due to this bacterium.