IntroductionThe prevalence of childhood infection with Helicobacter pylori is high, especially in developing countries. Non-invasive methods for detection of infection in children should be inexpensive, easy to perform, well tolerated and have a high diagnostic accuracy. We aimed to compare the reliability, specificity and sensitivity of the H. pylori stool antigen (HpSA) test with the 13C-urea breath test (13C-UBT) for the diagnosis of H. pylori infection in a limited resource setting.Material and methodsThe stool samples of 60 symptomatic and dyspeptic children with a mean age of 7.2 ±3.7 years (2–15 years) were evaluated using the rapid One step HpSA test by lateral flow immunoassay. The 13C-UBT was used as the gold standard method for the diagnosis of H. pylori infection.ResultsThe HpSA test detected H. pylori antigen in 34 out of 38 positive patients with 4 false-negatives (sensitivity 89.5%, 95% confidence interval (CI): 75.2–97.1%), while 21 patients had true-negative results and one false-positive (specificity 95.5%, 95% CI: 77.2–99.9%), with a strong measure of agreement between the HpSA test and the 13C-UBT (κ = 0.83, 95% CI: 68–97%, p < 0.001). It had a positive predictive value of 97.1% (95% CI: 85.1–99.9%), a negative predictive value of 84% (95% CI: 63.9–95.5%) and an accuracy of 91.7%.ConclusionsThe rapid lateral flow HpSA test is a reliable method for the primary diagnosis of H. pylori infections in children, though not as accurate as the 13C-UBT. It is more affordable, simpler to perform and more tolerable, representing a viable alternative, especially in developing countries.