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Objective Comparing health-related quality of life (HRQOL) in children suffering from functional and organic gastrointestinal disorders and to identify predictors for HRQOL. Methods Children with functional (n = 70) and organic (n = 100) gastrointestinal disorders, aged 8–18 years and referred to a pediatric gastroenterologist, completed questionnaires assessing pain severity, coping, and HRQOL. Results The sample reported low HRQOL scores, even significantly lower compared with reference values of chronically ill children, derived from normative data of KINDL-R, a generic QOL questionnaire. HRQOL was not significantly associated with age, gender, duration of pain, and diagnosis (functional gastrointestinal disorder vs. organic gastrointestinal disorder). Pain severity and catastrophizing were significantly associated with HRQOL, with catastrophizing fully mediating the relationship between pain and HRQOL. Conclusion The emotional burden associated with chronic abdominal pain—regardless of its cause—is enormous. Interventions should target the children’s coping strategies, as catastrophizing seems to be the causal link between pain and HRQOL.