CagA protein is encoded by the cagA gene, which is part of the cag pathogenicity island (PAI) in Helicobacter pylori. Insertion sequence (IS) elements are a diverse set of specialized DNA segments that can move to new sites in bacterial genomes. To determine the role of cagPAI and IS605 in the development of gastric cancer, we analysed cagPAI from patients with gastric cancer and compared the results with the host's CagA antibody status. H. pylori strains were isolated from 29 gastric cancer patients, and CagA status was determined by measuring serum antibody against CagA. The cagPAI region and IS605 were determined by PCR. CagA seropositivity tended to be higher in the IS605/PAI+ group (5/7, 71.4%) than in the IS605/PAI- group (9/22, 40.9%). Association with cag13 was more frequent in the IS605+ group (92.3%; 12/13) than in the IS605- group (25.0%; 4/16; P = 0.0005). cag13 may be associated with the presence of IS605 in gastric cancer patients.