Background & Aims The variation in size of Helicobacter pylori CagA is related to repeat sequences in the 3' region of the cagA gene. We investigated whether structural subtypes of the cagA 3' region are associated with presentation of the infection or to susceptibility to acid. Methods We examined 319 cagA-positive H. pylori isolates: 84 isolates from Bogota, Colombia; 83 from Houston, Texas; 24 from Siena, Italy; and 128 from Seoul, Korea. The cagA 3' region was amplified by polymerase chain reaction. Gastric histology and susceptibility to pH 3 were evaluated in relation to the number of cagA repeat regions. Results Strains with more than three repeat regions were associated with significantly higher scores for gastric mucosal atrophy and intestinal metaplasia than those with fewer repeat regions. H. pylori strains with three repeat regions were also significantly more susceptible to pH 3 than isolates with fewer repeat regions. ConclusionsH. pylori strains with more than three repeat regions in the 3' region of the cagA gene are associated with enhanced histological injury and with reduced survival in acidic conditions. It is hypothesized that these variants arise within the stomach.