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The aim of the study was to determine the current prevalence of Helicobacter pylori in symptomatic Colombian children and evaluate the presence of mutations associated with clarithromycin resistance. Biopsies from 133 children were analyzed. The gastric fragment was used for urease test and reused for polymerase chain reaction sequencing of the 23SrDNA gene. Mutations were detected by bioinformatic analysis. Polymerase chain reaction sequencing established that H pylori infection was present in 47% of patients. Bioinformatics analysis of the 62 positive sequences for 23SrDNA revealed that 92% exhibited a genotype susceptible to clarithromycin, whereas the remaining strains (8%) showed mutations associated with clarithromycin resistance. The low rate of resistance to clarithromycin (8%) suggests that conventional treatment methods are an appropriate choice for children. Recycling a biopsy that is normally discarded reduces the risks associated with the procedure. The 23SrDNA gene amplification could be used for a dual purpose: detection of H pylori and determination of susceptibility to clarithromycin.