Background & Aims: Diagnosis of Helicobacter pylori (HP) infection is based on invasive and noninvasive methods. The aim of this study was to determine the accuracy of stool antigen test in comparison with endoscopy and histology for detection of Helicobacter pylori in children. Materials & Methods: During four years, 233 children with gastrointestinal problems such as recurrent abdominal pain, vomiting, nausea, and failure to thrive referring to Ali-Asghar hospital enrolled in the study. Data was gathered and analyzed using SPSS. Results: Mean age of children was 7. 28 years (range 1-15 years). One hundred twenty five children (53. 6%) were female. In stool antigen test, positive and negative results were found in 134 (57. 5%) and 99 (42. 5%) patients, respectively. Also, pathology results revealed positive HP in 172 (73. 8%) cases and negative findings in 61 (26. 2%) cases. In present study, sensitivity, specificity, positive predictive value, and negative predictive value of fecal antigen test were 60. 4%, 50%, 77, 6% and 31. 3%, respectively. Conclusion: Results of this study showed that the fecal helicobacter pylori antigen test as a non-invasive method has low sensitivity and specificity in comparison to biopsy.