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Background/Aims To investigate the intra-rater (test-retest) reliability of the diagnosis of functional gastrointestinal disorders (FGIDs) as measured by the Questionnaire on Pediatric Functional Gastrointestinal Disorders, Rome IV version (QPGS-IV) in children. Methods A prospective cohort study was conducted in a public school in Cali, Colombia. Children and adolescents between 11 and 18 years of age were given the self-report Spanish version of the QPGS-IV at day 0 (baseline) and at day 2 (48 hours later). Results The study protocol was completed by 215 children, of which 97 (45%) were excluded from analysis due to the inability to follow the questionnaire's instructions. The final analysis included data of 118 children (mean age 15.0 ± SD 1.8 years old, 58.5% boys). The most common diagnoses were functional dyspepsia, functional constipation, and irritable bowel syndrome. We found a moderate intra-rater reliability (κ = 0.61-0.65) for diagnosing an FGID in general, a functional abdominal pain disorder, and the diagnosis of functional dyspepsia. We found a weak intra-rater reliability (κ = 0.46-0.54) for diagnosing a functional defecation disorder, functional constipation, irritable bowel syndrome, and the postprandial distress syndrome subtype of functional dyspepsia. Conclusions Our study shows that a large proportion of children cannot adequately complete the QPGS-IV and that the intra-rater reliability among those who did adequately follow the instructions is moderate. We advise to test the children's understanding of the instructions prior to completion of questionnaires and recommend to not rely exclusively on a self-reported questionnaire to select, recruit, or evaluate pediatric patients for FGIDs for research purposes. [ABSTRACT FROM AUTHOR]