The objective of current study was to detect the prevalence of Helicobacter pylori by identifying 16SrDNA and to determine the virulence genes (ureA, cagA and vacA) in biopsy specimens from patients suffering gastroduodenal disease using polymerase chain reaction (PCR). Forty samples were obtained by gastroenterologists during endoscopy from gastric antral of suspected individual attending endoscopy unit at Baqubah Teaching Hospital, Diyala, Iraq, during the period from September 2015 to February 2016. According to the endoscopic finding the patients were allocated into four groups of gastroduodenal diseases and control, which include gastritis (GS), duodenal ulcer (DU), gastric ulcer (GU), gastric cancer (GC), their rates were 30% (12), 20% (8), 17.5% (7), 7.5% (3) and 25% (10), respectively. DNA was extracted from the biopsies and subsequently used for PCR detection of H. pylori and the virulence genes using specific primers. The results shows that 60% of samples were positive for H. pylori, of these positive samples, 91,66%, 66.66%, and 48.83%, were shown to have the virulence genes, ureA, cagA, and vacA, respectively. It is important to mention that cagA shown the highest prevalence rate in gastric cancer cases in comparison with vacA gene. further studies are required to study the link between cagA gene and