Background: Helicobacter pylori (H pylori) is a major etiological agent in several gastroduodenal diseases. The most common virulence markers of H pylori are vacuolating cytotoxin (VacA), cytotoxin associated gene A (CagA), and blood adhesion binding antigen (BabA).
Objective: The study aimed to investigate the relation of VacA, CagA and BabA2 genotypes of H pylori strain to the endoscopic findings particularly (peptic ulcer or gastric carcinoma) in infected patients.
Patients, Materials and Methods: A cross sectional study was carried out in the clinical pathology department and Tropical Endoscopy unit at Faculty of medicine, Zagazig university..The study included 100 patients who attended the Endoscopy unit for Upper gastrointestinal endoscopy due to different complains (epigastric pain, heart burn, regurgitation, dyspepsia and vomiting. Two gastric biopsy samples were taken for Rapid Urease Test (RUT) and PCR.

Results: The study showed 62 out of hundred patients (62%) were H.pylori positive and 50 out of 62 H pylori positive cases (81%) revealed one or more virulent factor. The positive rate of VacA, CagA and BabA2 among H.pylori positive patients were 73%.23% and 26% respectively. The allelic variant Vac s2m2 was more prevalent 42% than other alleles. The most predominant genotype combination VacA/CagA 7/50 (14%) . VacA was found among 49% in cases of peptic ulcer. A statistically significant different between VacA, triple gene combination and the clinical outcome. P