Helicobacter pylori infection induces an increase in the rate of apoptosis in gastric epithelial cells and initiates a secondary hyperproliferative response. Currently, cytotoxin-associated proteins and vacuolating cytotoxin participate in the induction of the apoptotic process in the gastric epithelium, however, the existence of other factors that participate in this process has not been ruled out. Moreover, differential protein expression by H. pylori during the apoptotic process has not been studied. The aim of this work was to study differential H. pylori protein expression during the process of apoptosis in AGS cell. AGS cells were infected with H. pylori and apoptosis was determined by measuring chromatin condensation and caspase-3 activity. In addition, bacterial and cellular protein extraction was performed during apoptosis. The H. pylori protein profile was analyzed by double-dimension electrophoresis (2-DE) and protein identification was performed by LC/NSI-MS/MS analysis. A significant increase in chromatin condensation and caspase-3 activity was seen in the AGS cells 12 h post-infection. The proteomic analysis demonstrated a significant increase in the expression of 19 proteins, from which five proteins were identified from H. pylori. Thirty-one spots were present during the pathogen-host interaction. In conclusion: H. pylori induced a significant increase in apoptosis in infected AGS cells 12 h post-infection, and the H. pylori proteins that were identified could be participating in the apoptotic event.