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Background We previously detected Helicobacter pylori infection by stool antigen ELISA assay in 33-41% of asymptomatic Chilean children between 2-3 years of age, of which 11-20% had a transient infection and 21-22% a persistent infection. A total of 88% of ELISA-positive samples were also rt PCR positive, while 37/133 (33%) of ELISA-negative stool samples were rt PCR positive. The significance of a ELISA-negative/rt PCR-positive sample requires clarification. We aimed to determine whether rt PCR is able to detect persistent infections not detected by ELISA. Materials and Methods We selected 36 children with an ELISA-negative/rt PCR-positive stool sample, of which 25 were never H. pylori infected according to ELISA, and 11 had a transient infection with an ELISA-positive sample before or after the discordant sample. At least two additional consecutive ELISA-negative samples per child were tested in duplicate by rt PCR for the 16s rRNA gene. Results A total of 14 of 78 (17.9%) rt PCR reactions were positive, but only 4/78 (5.1%) were positive in both duplicates, representing a total of 3/36 (8.3%) children with an additional rt PCR-positive sample, only one of whom was persistently negative by ELISA. One child with a transient infection had two positive rt PCR reactions despite negative ELISA samples. Conclusions In H. pylori noninfected or transiently infected children, as determined by stool ELISA, additional ELISA-negative/rt PCR-positive stool samples were found in 8.3% of children, but a possible persistent infection was only identified in 2.7% of children. Thus, the characterization of infection dynamics in children is not being misrepresented by application of stool ELISA. Furthermore, rt PCR does not significantly improve dynamic characterization. [ABSTRACT FROM AUTHOR]