Previous studies have implicated CagA [encoded by cytotoxin-associated gene A (cagA)] in Helicobacter pylori-associated gastroduodenal pathology and distinct subgenotypes of cagA may circulate in different pathological manifestations of cagA-positive H. pylori infection. To investigate cagA genotype and variants in Chinese H. pylori strains and explore their relationship with gastroduodenal diseases, the cagA status of 82 Chinese H. pylori strains was examined and variation in size of the 3' region of cagA in 71 of these strains was analysed by PCR. cagA was detected in 28 (100%) of 28 strains from peptic ulcer patients, two (100%) of two strains from gastric cancer patients, 32 (94.1%) of 34 strains from chronic gastritis patients and 17 (94.4%) of 18 strains from healthy volunteers. PCR products of the cagA 3' variable region were obtained from 71 (92.2%) of 77 Chinese H. pylori strains and could be classified into subgenotypes I, II and III, which gave PCR products of around 825, 900 and 950 bp, respectively. Subgenotype I cagA predominated in Chinese H. pylori strains (67/71), whereas subgenotype II cagA presented in two isolates from patients with chronic gastritis and subgenotype III presented in two isolates from healthy volunteers. Therefore, neither cagA nor its 3' region variants can be used as a sole marker for the presence of particular H. pylori-related gastroduodenal diseases in the Chinese population.