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Background The Pasitos Cohort Study has followed children in El Paso, Texas and Ciudad Juarez, Mexico since 1998 to identify determinants of Helicobacter pylori infection. This paper describes patterns of acquisition and elimination of H. pylori infection in 468 children from birth to 24 months.Methods Mothers were recruited during pregnancy at maternal-child clinics; children were targeted for follow-up examinations every 6 months after birth. H. pylori infection was detected using the 13C-urea breath test, corrected for age-dependent variation in CO2 production.Results Test results were available for 359, 341, 269, and 215 children around target ages of 6, 12, 18, and 24 months, respectively. The person-time at risk of a first detectable infection was 7742 person-months; 128 first infections were detected, thus the incidence rate was 1.7% per month (95% confidence interval 1.42.0%). Rates were similar in boys and girls and on both sides of the border; evidence suggests, however, that this similarity could be due to selection bias. Among children with follow-up after a positive test, 77% tested negative at a later visit.Conclusions The initial acquisition of detectable H. pylori infection occurred at a rate of 20% per year among Pasitos Cohort children from birth to 24 months of age. A key finding, with implications for clinical, community health, and research settings, is that most of these infections did not persist. The transient nature of early H. pylori infection should be considered when designing research or contemplating therapeutic intervention for this age group. [ABSTRACT FROM AUTHOR]