Background: Some disease-specific Helicobacter pylori virulence genes can be used for predicting the outcome of diseases. Thus, the current study aimed to explore the frequency of the vacA, cagA, sabA, dupA, babA, oipA, and iceA1 genes in H. pylori isolates, and to determine whether any association exists between the expression of these genes and gastric cancer (GC).Methods: H. pylori isolates were collected from individuals with digestive diseases. The cagA, vacA, dupA, sabA, babA, oipA, and iceA1 genes were determined by PCR. The qRT-PCR was used for expression analysis of the tested genes. Results: The presence of the cagA, vacA, dupA, sabA, babA, oipA and iceA1 genes in H. pylori isolates were 41.3%, 95.5%, 31.0%, 93.1%, 55.1%, 82.7%, and 62.0%, respectively. The cagA, dupA, and babA expression in the GC patients was statistically higher than that of the control group (P <0.05). Conclusions: Our results indicated a high diversity and frequency of H. pylori virulence genes among individuals with gastric diseases in the Iranian population. The cagA, dupA, and babA expression were significantly higher in the GC patients, thus, it may suggest that screening of these genes may help identify peoples at higher risk for GC.