Background/Aims: Cytotoxin-associated gene (cagA) and vacuolating cytotoxin (Vac) production have been reported to be major virulence factors of Helicobacter pylori. We evaluated whether cagA genotype and Vac production might be correlated with gastroduodenal diseases in Korea and whether this correlation could be due to difference in proinflammatory cytokine expression and apoptosis of gastric epithelial cells. Methods: The presence of cagA gene and Vac production were examined after H. pylori was isolated from Korean patients. Gastric epithelial cells were infected with cagA+Vac+, cagA+Vac- or cagA-Vac- strains, and then, cytokine gene expression was evaluated using quantitative reverse transcription- polymerase chain reaction. Apoptosis and caspase-3 activation were measured in H. pylori-infected epithelial cells. Results: There was no significant correlation between the presence of those virulence factors in isolated H. pylori strains and peptic ulcer or gastric cancer. Upregulation of the cytokine gene expression, including interleukin (IL)-1α, IL-8, GM-CSF and monocyte-chemoattractant protein 1, as well as apoptosis and caspase-3 activation showed no difference due to the infection with cagA-positive and cagA-negative strains. Moreover, they were not correlated with the production of Vac. Conclusions: These results suggest that the non-correlation between virulence factors of isolated H. pylori strains and gastroduodenal disease entities in Korea is due to similar capacity in proinflammatory cytokine gene expression and apoptosis by each H. pylori strain infection.