Background: Detection of Helicobacter pylori antigen in stool samples has been a subject of controversy. However, it has been included in several clinical guidelines as a recommended non-invasive testing procedure in dyspeptic patients. Aim: To compare a monoclonal enzyme immunoassay for detection of H. pylori stool antigen (Amplified IDEIA HpStAR, DakoCytomation) with a polyclonal enzyme immunoassay (HpSA test, Premier Platinum HpSA, Meridian Diagnostics) in diagnosing infection and in determining H. pylori status after eradication treatment. Methods: We evaluated stool samples of 198 patients diagnosed with H. pylori infection and of 41 patients without infection. The results of the monoclonal enzyme immunoassay HpStAR were compared with those of the polyclonal enzyme immunoassay HpSA. Results: The sensitivity and specificity of HpStAR were 91.9% and 70.7%, while those of HpSA were 89.4% and 80.5%, respectively. In the 126 patients evaluated 6 weeks after eradication therapy, the overall agreement between urea breath test and HpStAR was 90.5% (P = 0.710) and between urea breath test and HpSA was 76.9% (P = 0.410). Conclusions: HpStAR is a rapid and easy-to-perform test with similar sensitivity to HpSA in the diagnosis of H. pylori infection, although it had lower specificity. In contrast, HpStAR is more accurate after eradication therapy than HpSA. © 2006 Blackwell Publishing Ltd.