Background & Objectives: Today, various evidences indicate that Helicobacter pylorus is one of the significant factors in gastric ulcer and duodenal ulcers. This bacterium, which is seen in mucousal layer and in vicinity of epithelial cells causes, mucousa changes, cell disorders, tissue lesions, and inflammation. One of the important characteristics of this bacterium is producing large amounts of urease enzyme. The activity of urease enzyme can be an important virulence factor which plays a key role in causing damage to mucousa, and replacement of bacterium in mucousa of stomach. In this study, the role of urease enzyme in causing cell lesions was investigated. Methods: The study was carried out on 100 biopsy specimens. A speedy urea test was performed in endoscopy theatre, for all these samples. The biopsy samples were transferred to the laboratory in transport medium and were cultured in the selected medium. Then, the identification of bacteria was done by microscopic examination and biochemical tests. The cultures of 80 samples of biopsy were positive. The direct effect of supernatant containing urease enzyme extracts from 50 bacterium samples on HeLa cell. was investigated. Furthermore, urea with concentrations of 3.75 and 20 m.molar as well as enzyme containing supernatant were added to HeLa cell culture medium. To investigate the factors causing cell lesions, ammonia was used in PBS with concentrations of 40, 32, 22, 20, 15, 10, 8, 7 and 3 m.mol. Results: In the presence of urease enzyme and a concentration of 20 m.molar of urea, the colour of the culture medium turned into purple. This change was a sign of the production of large amounts of ammonia. Intracellular vacuoles were formed as well. By adding urease enzyme containing supernatant in the absence of urea, intercellular vacuole was not observed. Neither in concentrations of below 8 m.molar of ammonia was intercellular cell vacuole observed. While, in concentrations over 8 m. mol. the cytopathic effect was observed in the form of vacuoles, and in the concentration of 40 m. mol. of ammonia, the full erosion of cell layer occurred.Conclusion: Therefore, based on the results of this investigation, urease enzyme in not directly harmful. It is the ammonia produced as a result of hydrolyze of urea by urease enzyme which has toxic effects and causes inflammation and ulcers.