The proteins expressed in gastric epithelial cells infected with Helicobacter pylori (H. pylori) may determine the clinical outcome such as chronic gastritis, peptic ulcer, and gastric carcinoma. The present study aims to determine the differentially expressed proteins in human gastric epithelial AGS cells that were infected with H. pylori in a Korean isolate, a cagA+, vacA s1b m2 iceA1 H. pylori by proteomic analysis. The differentially expressed proteins, whose expression levels were more or less than twofold in H. pylori-infected cells, were analyzed. Ten proteins (chromatin assembly factor-1, proliferating cell nuclear antigen, 14-3-3 protein tau, eukaryotic translation initiation factor 6, heat-shock protein 90 beta, dimethylarginine dimethylaminohydrolase-1, l-lactate dehydrogenase B chain, prohibitin, triosephosphate isomerase, protein disulfide isomerase) were up-regulated while eight proteins (heat-shock gp96 precursor, nucleophosmin, ornithine aminotransferase, Ku70, l-arginine-glycine amidinotransferase, Smad anchor for receptor activation, ADP-ribosylation factor, WD repeat-containing protein isoform 1) were down-regulated by H. pylori infection in AGS cells. These proteins are related to cell proliferation, cell adhesion, carcinogenesis, cell-defense mechanisms against oxidative stress, membrane trafficking, and energy metabolism. Oxidative stress, cell proliferation, cell adhesion, and membrane trafficking may be involved in the pathogenesis of gastric diseases including cancer associated with H. pylori in a Korean isolate.