Helicobacter pylori (H. pylori) infection is one of the most common causes of gastritis and peptic ulcer diseases. A risk association between H pylori infection and the development of gastric adenocarcinoma and mucosa associated lymphoid tissue lymphoma has been established. H. pylori reside in the gastric mucus layer of the superficial epithelium, attachs to gastric epithelial cells and mucins are the most important structural component of the mucus gel layer. Methods that accurately detect H. pylori infection in dyspeptic patients are therefore of major importance. AIMS: This study aimed to assess the diagnostic accuracy of H. pylori stool antigen (HpSA) test by enzyme immunoassay (EIA) compared with the standard methods of diagnosis and to determine the antimicrobial sensitivity of isolated strains. Also; to study the effect of H pylori on gastric MUC5AC and MUC2 protein expression by immunohistochemistry as a prognostic tool of gastritis progression. METHODS: The study included 62 selected patients who underwent upper endoscopy for evaluation of dyspeptic symptoms. Gastric biopsy samples were taken for culture and histopathology; MUC2 & MUC5AC immunostaining expression. Stool samples were also collected from all the patients for the detection of H. pylori antigen using polyclonal EIA. RESULTS: The total number of helicobacter positive cases was 42/62 (67.7 %); 34 of them (54.8%) of them had both positive culture and histology. H. pylori was identified in 40/62 (64.5%) gastric biopsy samples by culture and 36/62 (58.1%) by histopathology, Gemisa stain. Antimicrobial resistance of the 40 H. pylori isolated to mitronidazole, clarythromycin, amoxicillin, tetracyclines was 100%, 20%, 57.5%, and 5% respectively. The HpSA test was positive in 36/42 (85.7%) patients with H. pylori infection as determined by standard methods and negative in 16/20 (80%) of non infected patients. The sensitivity and specificity of HpSA test were 85.7 % and 80 % respectively while the negative and positive predictive values were 72.7 % and 90 % respectively. The overall diagnostic accuracy was 83.8 %. In H. pylori infected patients the MUC5AC-expression and its staining intensity was completely absent in 8/42 (19%), mildly expressed in 12/42 (28.6%), moderately expressed in 22/42 (52.4%) of them. Strong MUC5A expression was only found in all H pylori negative cases.  The staining pattern of MUC2 was positive in 18/42 (42.9%) of Helicobacter pylori positive patients. All MUC2 positive cases displayed only mild positive stain. Conclusion: HpSA EIA is a non invasive, rapid, easily performed, reliable method for accurate diagnosis of H. pylori infection. Clarytheromycin containing triple regimens may be prefered to metronidazole containing triple regimens in our local population. Changes in gastric mucin are a useful diagnostic tool of disease progression in patients suffering from dyspepsia due to helicobacter gastritis and may even be detected before histopathological changes (dysplasia, intestinal metaplasia, ulceration or malignancy)