BACKGROUND: Egypt considered a highly endemic country for H.pylori, it’s associated with gastritis, peptic ulcer disease and gastric cancer. Stool antigen test considered as a non-invasive reliable test. Salivary PCR considered is a new modality for diagnosis of H.pylri. AIM: To evaluate the validity of salivary PCR test in diagnosis of H.pylori. METHODS: This study included 50 patients’ attendants of Gastrointestinal Endoscopy Unit Faculty of Medicine, Cairo University. They all proved histologically to have H.pylori induced gastric and/ or duodenal pathology. All underwent stool antigen test and salivary samples for H. pylori PCR. RESULTS: Prevalence of H.pylori in symptomatizing Egyptian patients was 62.5%. Patients were middle aged (mean age was 42.0 ± 11.6 years old), and comparable gender presentation (54% females versus 46% males). the commonest endoscopic findings were gastric affection (90%), and duodenal affection (44%), third of cases (34%) showed definite ulcer lesions. Interestingly, none of the patients had either complicated peptic ulcer disease, or malignant growth. Sensitivity of SAT was 82%, and was significantly related to epigastric pain, the commones complaint, but was not related to the endoscopic finding. The sensitivity of H.pylori Salivary PCR test was 100%, and it displayed wide range of results; mean value 10179.0 copies/dl and median 4020.5 copies/dl. No significant relation with either the symptomatizing complaint or with the endoscopic finding. CONCLUSION: Salivary PCR assay showed 100% sensitivity in diagnosing H. pylori, thus considered a reliable diagnostic test, however, it showed a very wide range of level in diagnosis with no definite differentiating cut off level regarding complaint, SAT or endoscopic finding.