We evaluated an antigen-based stool assay as an indicator of Helicobacter pylori (Hp) status during treatment aimed at eradicating Hp in 22 Hp-positive patients and 63 negative control patients. The sensitivity and specificity of the assay was 100% and 70%, respectively, when the manufacturer's cutoff was used. When we used the cutoff calculated from a receiver operating characteristic curve, the specificity of this test increased. Under these conditions, the test could be used in monitoring treatment and verifying eradication of Hp infection. Further studies must be carried out to standardize the cutoff in children.