Background: Helicobacter pylori is the main cause of various gastroduodenal diseases. As the diseases caused by H. pylori are associated with severe tissue damage, proteases of bacteria may play an important roles in this process. In current study we investigated diversity of H. pylori protease activity and its association with different pathological lesions of gastric tissue. Materials & Methods: The study was performed on 116 gastric biopsy specimens obtained from patients with gastrointestinal disorders referred to Taleghani hospital in Tehran, IR.Iran. Isolates were identified by culture and polymerase chain reaction (PCR). Their protease activity was assessed by spectrophotometric and well diffusion assays using casein as substrate. Variance analysis (One-way ANOVA) was used for statistical analysis. Results: A prevalence of 43.1% (50/116) of H. pylori infection was detected in the studied patients. Histopathological lesions among 50 H. pylori positive patients were included: chronic gastritis 40% (20/50), intestinal metaplasia 8% (4/50), and severe active gastritis 52% (26/50). Nearly, 4.25% of the strains showed high protease activity, while 91.4% and 4.25% of the strains showed moderate and low protease activities, respectively. Statistical analysis demonstrated significant association between low protease activity of the strains and chronic gastritis (p= 0.044). Conclusion: Results of this study indicated diversity of protease activity among different strains of H. pylori and significant association between low protease activity of the strains and occurrence of chronic gastritis. Further studies are necessary to investigate this association.