The occurrence of cagA and vacA alleles among Helicobacter pylori isolates from Turkish patients and their relationship with ulcer disease outcome was investigated. Among isolates from 47 patients with peptic ulcer disease and 51 patients with non-ulcer dyspepsia, 72.3% and 44.4%, respectively, were cagA-positive (p 0.019). Most (88.8%) isolates were typed as vacA s1, and all of these were subtype s1a. The commonest (51.0%) vacA genotype was s1a m1. The results of multivariate analysis indicated that infection with cagA-positive H. pylori was the only variable associated with an increased risk of peptic ulcer disease (odds ratio, 3.01; 95% confidence interval, 1.27-7.10; p 0.012).