OBJECTIVE: To compare health-related quality of life (HRQOL) in pediatric patients with functional gastrointestinal disorders (FGIDs) and organic gastrointestinal (GI) diseases with an age-, sex-, and race/ethnicity-matched healthy sample across GI diagnostic groups and with one another. STUDY DESIGN: The Pediatric Quality of Life Inventory 4.0 Generic Core Scales were completed in a 9-site study by 689 families. Patients had 1 of 7 physician-diagnosed GI disorders: chronic constipation, functional abdominal pain, irritable bowel syndrome, functional dyspepsia, Crohn's disease, ulcerative colitis, and gastroesophageal reflux disease. The healthy control sample included 1114 families. School days missed, days in bed and needing care, parent missed workdays, work impact, and healthcare utilization were compared as well. RESULTS: Patients with an FGID or organic GI disease demonstrated lower HRQOL than the healthy controls across all dimensions (physical, emotional, social, and school; P < .001 for all), with larger effect sizes for patients with an FGID. Patients with an FGID manifested lower HRQOL than those with an organic GI disease. Patients with an FGID or organic GI disease missed more school, spent more days in bed and needing care, had greater healthcare utilization, and had parents who missed more workdays with greater work impact (P < .001 for most), with larger effect sizes for the patients with an FGID. CONCLUSION: Patients with an FGID or organic GI disease demonstrate impaired HRQOL compared with healthy children. HRQOL can be used as a common metric to compare patient outcomes in clinical research and practice both within and across groups of patients with FGIDs and organic GI diseases.