Peptic ulcer disease incidence is decreasing. Both s1m1 and s1m2 vacA gene combinations of Helicobacter pylori have been associated with the development of major gastroduodenal diseases. This study assessed whether H. pylori vacA gene arrangement changed over 15 years in a Southern Italy area. H. pylori-positive patients observed in January-June 1989 and January-June 2005 were selected. Histological specimens were retrieved to extract DNA for vacA arrangement characterization (mid-m and peptide signal-s regions) by using the polymerase chain reaction. Fifty-nine patients in the first period and 56 matched patients in the second period were evaluated. A correlation between s1 presence and intestinal metaplasia at histology was found. Overall, the s1m1 combination increased (P < 0.01) and s2m2 decreased (P < 0.001) during the study period. In detail, s1m1 (P < 0.05) and s1m2 (P < 0.01) increased, and s2m2 decreased (P < 0.001) in dyspeptic patients, while only s1m1 increased (P < 0.01) in peptic ulcer patients. Finally, few cases of s2m1 combination in both series were found. Our results show some unexpected aspects that require confirmation. In detail, the increased prevalence of potential more virulent H. pylori strains contrasts with peptic ulcer incidence reduction.