Two virulence factors encoded by the cytotoxin-associated (cagA) gene and the vacuolating toxin (vacA) gene of Helicobacter pylori are known to be associated with gastroduodenal pathologic conditions. In this report, nucleotide sequence of cagA and vacA and the serum antibody response to the CagA antigen in H. pylori isolates from Taiwanese patients were studied.cagA and vacA were characterized in 173 H. pylori strains by polymerase chain reaction and DNA hybridization analyses. The presence of serum IgG antibodies against CagA was assessed by Helico-blot Western blot system. Sequence analysis of polymerase chain reaction-amplified vacA and cagA was performed for two strains.cagA was detected in all the isolates with peptic ulcers and gastric cancer. Of 54 strains with non-ulcer dyspepsia, 51 were found to be cagA+. Serum antibodies to CagA were detected for 99.2% of cagA+ strains compared with 0% of strains lacking cagA. vacA was detected in all isolates. Sequence analysis of vacA and cagA indicated that sequences of two Taiwanese strains were closely related to each other (95.9% and 97% nucleotide identity, respectively) but less homologous to the published strains (90.9% and 91.4% mean nucleotide sequence identity, respectively).The strong association (98%) of cagA+ strains with Taiwanese patients suggests that the cagA+ phenotype could not be used as a single marker of high-risk patients in Taiwan. Moreover, sequence analysis indicates that Taiwanese strains contain different genetic sequences from those in other geographic regions.