The cytotoxin-associated gene (cag) pathogenicity island (PAI) is important for the virulence of Helicobacter pylori. In this study, we have compared the complete nucleotide sequence of the cag PAI in four clinical isolates. These isolates were selected from patients matched for age and sex from the same geographical region. The patients suffered from either gastric cancer (Ca52 and Ca73) or duodenal ulcer (Du23:2 and Du52:2). All four strains induced an interleukin (IL)-8 response in AGS cells and translocated CagA into host cells where the protein was tyrosine phosphorylated, and thus harboured a functional type IV secretion system encoded by the cag PAI. The cagA gene contains a variable region close to its 3' end. Different compositions of this region has been proposed to exert various degrees of morphological changes in cultured gastric epithelial cells, and there are indications that the structure of the repetitive region is connected to the severity of disease. One of the studied strains (Du23:2) possessed five Western-type repeat regions while the other three strains harboured one Western-type repeat. Strain Du23:2 also contained a major rearrangement or large insertion/duplication in the intergenic region between HP0546 and HP0547 (cagA). Sequence similar to that of genes HP0510 and HP0509 was found in the 5' end of this region. The 3' end was similar to the corresponding region of strain ATCC 43504, including a mini IS605 element and a duplication of the 3' end of the cag PAI. Finally, a novel gene was identified in the cag PAI in three of the sequenced strains at the position of HP0521. This gene, HP0521B, is present in approximately half of Swedish H. pylori isolates.