The interrelationship between cytotoxin-associated gene A (CagA), vacuolating cytotoxin (VacA), and Helicobacter pylori-related diseases was investigated in 155 H. pylori-infected patients. Four (7%) of 60 subjects had mixed cagA+ and cagA- H. pylori infections. The H. pylori isolates from 98.3% of 121 patients with anti-CagA antibodies were cagA+. The occurrence of cagA+ H. pylori among 76 patients with peptic ulcer disease (PUD) was higher (93.4%) than among 79 patients with functional dyspepsia (FD; 64.6%) (odds ratio [OR] = 7.80; P < .001). VacA+ isolates were isolated from 56.6% of the PUD patients and 35.4% of the FD patients (OR = 2.37; P = .0132). For type I (cagA+VacA+) isolates, these numbers were 56.6% and 31.6%, respectively (P = .003). Only 4% of the 71 VacA+ isolates were cagA-. In addition, 37% of the patients with PUD were infected with cagA+VacA- H. pylori. Chi 2 results did not improve when VacA was entered into the model in the presence of cagA, indicating that only cagA is associated with PUD.