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Objective The present study investigates the clinical interpretability of the Pediatric Quality of Life Inventory™ (PedsQL™) Gastrointestinal Symptoms Scales and Worry Scales in pediatric patients with functional gastrointestinal disorders or organic gastrointestinal diseases in comparison with healthy controls. Methods The PedsQL™ Gastrointestinal Scales were completed by 587 patients with gastrointestinal disorders/diseases and 685 parents, and 513 healthy children and 337 parents. Minimal important difference (MID) scores were derived from the standard error of measurement (SEM). Cut-points were derived based on one and two standard deviations (SDs) from the healthy reference means. Results The percentages of patients below the scales’ cut-points were significantly greater than the healthy controls (most p values ≤ .001). Scale scores 2 SDs from the healthy reference means were within the range of scores for pediatric patients with a gastrointestinal disorder. MID values were generated using the SEM. Conclusions The findings support the clinical interpretability of the new PedsQL™ Gastrointestinal Symptoms Scales and Worry Scales.