Accurate noninvasive tests for diagnosing Helicobacter pylori infection in very young children are strongly required. We investigated the agreement between the [13C]urea breath test ([13C]UBT) and a monoclonal ELISA (HpSA) for detection of H. pylori antigen in stool. From October 2007 to July 2011, we enrolled 414 infants (123 from Brazil and 291 from Peru) of ages 6 to 30 months. Breath and stool samples were obtained at intervals of at least 3 months from Brazilian (n=415) and Peruvian (n= 908) infants. [13C]UBT and stool test results concurred with each other in 1,255 (94.86%) cases (kappa coefficient=0.90; 95% confidence interval [CI]-0.87 to 0.92). In the H. pylori-positive group, delta-over-baseline (DOB) and optical density (OD) values were positively correlated (r=0.62; P<0.001). The positivity of the tests was higher (P<0.001; odds ratio [OR]=6.01; 95% CI-4.50 to 8.04) in Peru (546/878; 62.2%) than in Brazil (81/377; 21.5%) and increased with increasing age in Brazil (P= 0.02), whereas in Peru it decreased with increasing age (P<0.001). The disagreement between the test results was associated with birth in Brazil and female gender but not with age and diarrhea. Our results suggest that both [13C]UBT and the stool monoclonal test are reliable for diagnosing H. pylori infection in very young children, which will facilitate robust epidemiological studies in infants and toddlers. Copyright © 2013, American Society for Microbiology. All Rights Reserved.