The aim of the study was to determine inter- and intrapatient variation of Helicobacter pylori strains based on genomic fingerprinting and cagA (cytotoxin-associated gene A) status. Ten bacterial colonies from each of 10 patients with gastric cancer (GC), 10 with duodenal ulcer (DU), and 10 with gastritis (GI) were used. The presence of the putative adhesin gene, the cagA gene, and the strain specific banding pattern obtained by arbitrary primed (AP-) PCR was analyzed. Genomic fingerprinting showed extensive interpatient variation, but the banding patterns obtained from colonies from the same patient were always identical (intrapatient variation). In five patients, the cagA status varied between the colonies despite identical banding patterns. Among patients in a developed country such as Sweden, the proportion with multiple-strain infection of H. pylori is low, but subclones with differing cagA status exist within the strain.