Purpose: Helicobacter pylori (H. pylori) infection causes gastric inflammation and gastritis which increase the risk for peptic ulcer disease (PUD). Several genes of H. pylori such as cagA, vacA and iceA genes may play an important role in pathogenesis of this disease. The aim of this study was to examine the prevalence of genes cagA, vacA and iceA of H. pylori in patients with PUD compared with patients with non-ulcer dyspepsia (NUD) and to determine the association of these genes with PUD. Methods: In this study, 40 H. pylori isolates were obtained from PUD patients and 40 isolates from NUD patients. Genes cagA, vacA and iceA of H. pylori were identified by using polymerase chain reaction (PCR) with specific primers. Results: The result of this study demonstrated that cagA positive, vacA s1, m2 and iceA2 genes were found predominantly in H. pylori in Thailand. The presence of either cagA, allelic variant vacA and iceA alone does not have a predictive value as a risk marker for clinical outcome of H. pylori infection. In addition, high prevalence of mixed iceA isolates (48.75%) was found in Thai patients. All of these isolates contained single vacA genotype which suggests the presence of mixed iceA genotype in one strain. From analysis, vacA s1a, mixed iceA genotype was found to be significantly associated with PUD (P = 0.04, OR = 2.51, 95%CI = 1.05–6.04). Conclusions: Genes vacA s1a and mixed iceA genotype may play important roles in the pathogenesis of peptic ulcer disease and might be regarded as marker for predicting peptic ulcer disease in Thailand.