BACKGROUND Epidemiological studies suggest a negative association between Helicobacter pylori and gastro-oesophageal reflux disease (GORD). Moreover, cagA-positive strains are reported to protect from complications of GORD. The aim of this study was to determine virulence factors (cagA, vacA and iceA) of H. pylori strains and the pattern of gastritis in patients with GORD in comparison with patients with duodenal ulcer (DU) or functional dyspepsia (FD). METHODS H. pylori strains isolated from gastric biopsies of 105 consecutive patients with mild to moderate erosive GORD (n = 35, LA grade A-B), and from sex- and age-matched patients with DU (n = 35) or FD (n = 35 without reflux symptoms) were investigated. CagA, vacA, and iceA genotypes were determined by PCR analysis of the isolates. Gastritis was classified in accordance with the updated Sydney classification. RESULTS The prevalence of all three H. pylori virulence factors was higher in patients with GORD (cagA+ 80%, vacA s1 77%, iceA1 71%) and DU (cagA+ 83%, vacA s1 80%, iceA1 74%) than in patients with FD (cagA+ 40%, vacA s1 49%, iceA1 46%). Gastritis activity in the antrum and corpus did not differ between the three groups. However, lymphocytic infiltration of the gastric antral mucosa was more pronounced in DU patients than in those with GORD or FD. CONCLUSIONS H. pylori strains obtained from patients with mild to moderate erosive GORD show a virulence pattern similar to that found in DU patients. The presence of these virulence factors does not appear to protect against erosive lesions in the oesophagus.