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Serologic methods to detect Helicobacter pylori in infants, especially in developing countries, may be limited because of decreased immune response caused by malnutrition. The true prevalence may therefore be underestimated in this age group. Urea breath test is considered to be a good screening method in children but is expensive and therefore is not suitable for screening in developing countries. Simple, inexpensive, and accurate noninvasive methods to detect H. pylori in infants and young children are needed.Enzyme immunoassay (EIA) and immunoblot (IB) serologic analyses, 13C-urea breath test (UBT), and immunomagnetic separation-polymerase chain reaction (IMS-PCR) were performed on stool specimens, to detect H. pylori in 68 children between 4 and 24 months of age (mean, 11.5 months) in an endemic area in Bangladesh and the results compared.The occurrence of H. pylori was 57% (n = 39) using only UBT, 60% (n = 41) using only IMS-PCR, and 78% (n = 53) using UBT and IMS-PCR together. The concordance between UBT and IMS-PCR results was 62%. Immunoblot was positive in only 9% (n = 6). Results in all 68 children were negative using EIA.The prevalence of H. pylori infection in this peri-urban community and age group was high. Only serologic methods seem to be unsatisfactory for screening of H. pylori infection in infants and may not reflect the true prevalence. Immunomagnetic separation-PCR is a simple and rapid method for detection of H. pylori in stool and is an attractive method for analysis of colonization in infants. However, it may reflect a different stage of disease than UBT. Further studies are needed to clarify this.