Background: Despite that most H. pylori infections are asymptomatic, some can develop major diseases like peptic ulcer and adenocarcinoma of stomach. Objectives: This study aimed to study the prevalence of H. pylori using real time PCR. Furthermore, detection of the cagA, iceA1, iceA2, vacA virulence genes and their relationship to clinical and histopathological alterations.Methods: Two gastric specimens were taken from every patient endoscopically, one of them was sent to histopathological analysis and the second biobsy was minced into tiny parts for real time PCR assay. Results: The results revealed that the prevalence of H. pylori was 66.67%. Thirty one (50%) of the studied strains harbored cagA gene. IceA gene was positive in 41.94%. The vacA gene was detected in all 62 (100%) samples. Many vacA gene subtypes were detected, the highest found was s1as1bm 20.97%. A significant association was detected between the endoscopic features and vacA presence. The subtypes of vacA: s2, m2,s1a1b, s1as1bm2, were related to gastritis, while s1a, s1b, m1were related to duodenal and stomach ulcers. No significant association between cagA presence and endoscopical or histopathological findings, but more than 66% of duodenal ulcers had positive cagA gene. There was a significant association between the iceA1 and iceA2 genes presence with gastritis and gastric ulcer. Conclusion the study of H. pylori virulence factors allows the clinician to identify high-risk patients caused by H. pylori infections.