Helicobacter pylori infection is a widespread problem all over the world. It is the major cause of peptic ulcer disease and gastric carcinomas. Among the various methods available in clinical practice are histopathology, rapid urease test (RUT), cultureand PCR carried on gastric biopsy samples.Non-invasive diagnostics like stool antigen detection are available for rapid diagnosis and treatment follow up. The purpose of the study was to validate antigen detection of H.pylori from stool specimen and also to compare the test with that of rapid urease test and histopathology. This cross sectional case study was conducted on 260 subjects with symptoms of acid peptic disease who underwent endoscopic examination and not on non steroidal anti-inflammatory drugs or proton pump inhibitors. Gastric biopsy specimen and the stool samples were collected from patients with mucosal changes. Biopsy sample was subjected for Histopathological examination and Rapid urease test. Stool Antigen detection test was performed by immunochromatography method. Among the 260 study subjects stool antigen detection was positive in 184(70.7%) of the study population. H.pylori was detected by Rapid Urease test in 225(86.5%) of the patients while Histopathological examination identified H.pylori in 230(88.46%) by Haematoxylin and Eosin (H&E) staining and 235(90.38%) by Giemsa staining respectively. The sensitivity, Specificity, Positive predictive value and negative predictive value of Stool antigen detection when compared to Biopsy results were 78.29%, 100%, 100% and 32.89% respectively. The non invasive tests like stool antigen tests for H.pylori could be used as a routine diagnostic tool in the microbiology laboratory. The lower sensitivity of the stool antigen detection in comparison to histopathology and RUT is the drawback that has to be overcome.