The study evaluated a non-invasive antigen test of stool samples for the diagnosis of Helicobacter pylori infection in children compared with histopathology of gastric biopsies (gold standard). The study included 96 children aged 1-15 years old with dyspeptic symptoms referred for endoscopy at Tabriz Children's Hospital, Tabriz, Islamic Republic of Iran from May 2003 to March 2004. Of 62 children who were positive by histology, 34 were H. pylori stool antigen positive and of 34 patients with negative histology, 27 had negative stool test. The sensitivity and specificity of the test were low (54.8% and 79.4% respectively) compared with the gold standard and the positive and negative predictive values were 82.9% and 49.9%. However, the test may be useful for mass screening for H. pylori.