Helicobacter pylori infection is a widespread problem all over the world. Non-invasive techniques are demanded for rapid diagnosis and treatment follow up. The aim of this study was to compare the diagnostic value of phenol red chromo-endoscopy and stool (Rapid Strip HpSA) for H. pylori detection with reference to histopathology as the gold standard. A total of 80 adult patients with dyspepsia were enrolled on this study. Patients underwent phenol red chromo-endoscopy. Multiple Gastric biopsies were taken and examined for H. pylori detection. Stool sample was collected from every patient for Rapid Strip HpSA test. The study included 38 males (47.5%) and 42 females (52.5%) with their ages ranged between 19 and 56 years. According to histopathology, 71 patients (88.8%) were H. pylori positive and 9 (11.2%) were negative, most of biopsies showed inflammation with variable degree of activity, which showed significant statistical correlation with the density of H. pylori (P < 0.05). Phenol red chromo-endoscopy had 90.1% sensitivity, 88.9% specificity, 98.5% positive predictive value (PPV), 53.3% negative predictive value (NPV) and 90% accuracy. Rapid Strip HpSA had a sensitivity 93%, 77.8% Specificity, 97.1% PPV, 58% NPV and 91.3% accuracy. In conclusion; Phenol red chromo endoscopy was more specific and less sensitive than the rapid stool Rapid Strip HpSA® test regarding the detection of H. pylori infection with reference to histopathology as a gold standard, yet both showed high diagnostic accuracy; thus they can be used as reliable diagnostic tools for H. pylori infection in cases contraindicated for gastric biopsy.