H. pylori infection is pathologically involved in the development of gastric cancer. This study aimed at investigating the relationship between the genotypic characterization among gastric cancer patients and its comparison to patients with mild gastritis. Thirty gastric cancer patients and thirty patients with mild gastritis are enrolled in this study. H. pylori was cultured from 100% of cancer and gastritis patients. All isolated strains were resistant to metronidazole whereas tetracycline was the most effective antimicrobial agent. Extraction of H. pylori DNA and identification of its pathogenic genes, namely cagA, vacA and iceA were done by PCR and gel electrophorises. There was a significant association between certain virulent genes like cagA and some alleles of vacA and cancer stomach. This study also proved the presence of multiple genotypically diverse strains in the same patient. Positive association between cagA+ and vacA+ strains was also found. This findings may be important in predicting the clinical outcome of H. pylori infection among Egyptian patients.