Virulence factors produced by Helicobacter pylori have been known to be associated with serious gastroduodenal diseases. The aims of this study were to clarify the apoptosis-inducing properties of vacuolating cytotoxin (VacA) and examine the expression of apoptosis related proteins in human epithelial carcinoma cells expressing (AGS) or lacking (Kato III) p53. The midregion VacA homolog from H. pylori strain Q35 (Korean isolate) was cloned, expressed and sequenced. Recombinant VacA (VacA(418-799)) inhibited cell growth and induced apoptosis in gastric epithelial cells. Treatment with VacA(418-799) resulted in morphological changes and DNA fragmentation. Cell cycle analysis revealed subdiploid cells suggesting apoptosis, which was confirmed by the activation of caspase-3 and cleavage of PARP. VacA(418-799) also mediated a prolongation of the cell cycle progression in G1 phase. Furthermore, VacA(418-799) increased the expression of p53, p21(waf1/cip1) and Bax in AGS cells, but not in Kato III cells and did not affect the phosphorylation of Rb in both cell lines. These results indicate that recombinant VacA of H. pylori induces apoptosis in both Kato III and AGS cells, regardless of p53 status and suggest that VacA(418-799) mediate the development of gastric diseases through cell cycle arrest in the G1 phase. VacA(418-799) induction of apoptosis is associated with up-regulation of p53, p21(waf1/cip1), Bax in AGS cells and activation of caspase-3 in both cell lines.