Abstract: The aim of this study was to investigate the prevalence of cagA and cagE genes in H. pylori strains isolated from different patient groups with Non-Ulcer Dyspepsia (NUD), Duodenal Ulcer (DU), Gastric Ulcer (GU) and Gastric Cancer (GC). The patients admitted to the gastroenterology unit at Sharyati hospital in Tehran in 2006 were included in this study. Gastric biopsy specimens were obtained from the antrum of the stomach from each patient then cultured for detection of H. pylori. Identification of H. pylori was performed according to the standard bacteriological methods. Genomic DNA was extracted using a commercially available Qia gene kit. PCR was done using primers cagA-F, cagA-R and cagE-F, cagE-R to detect the target genes cagA and cagE, respectively. Amplified products of target genes were confirmed by sequencing. The cagA and cagE were detected among 85 and 86% of H. pylori isolates, respectively. Prevalence of cagA and cagE genes in the patients with NUD, DU, GU and GC were 22 (64.7%), 28 (100%), 18 (90%), 10 (100%) and 25 (73.5%), 27 (96.4%), 19 (95%), 7 (70%), respectively. The current study demonstrated a significant correlation between peptic ulceration and the presence of H. pylori isolates carrying cagE and cagA genes in Iranian patients.