BACKGROUND: Saliva is considered an important vector for the Helicobacter pylori infection. The presence of the babA2 gene, encoding for BabA (blood-group antigen binding adhesin), in the H. pylori genome is crucial for H. pylori-related pathogenesis. METHODS: The study was performed in the group of 215 patients. The detection of H. pylori and babA2 in saliva and gastric tissue was done by PCR (polymerase chain reaction). Moreover, gastric tissues were stained with hematoxylin-eosin as well as with modified Giemsa methods for the analysis of Helicobacter pylori density. RESULTS: The positive rate of H. pylori by nested PCR was 78.6% in gastric tissue and 72.7% in saliva. In addition, the positive rate of H. pylori was 55.5% by the histological analysis of Helicobacter pylori density in gastric tissue. The positive rate of babA2 by PCR was 33.9% in gastric tissue, and 8.2% in saliva. CONCLUSION: We revealed that the H. pylori PCR results obtained in gastric tissue correlated well with those obtained in saliva. As saliva is more available specimen, it is more suitable for clinical application of H. pylori detection by PCR. However, clinical use of - BabA PCR seems to be limited because of its low-sensitivity.