Functional gastrointestinal disorders (FGIDs) are common. The poor health-related quality of life in FGIDs is a combination of gastrointestinal symptoms and comorbid conditions. We determined by using the Ohio Dysautonomia questionnaire the medical comorbidities in 38 children with FGID. Almost all of the subjects had a comorbid disorder, with orthostatic symptoms in 89%, fainted >3×/lifetime in 17%, headaches with migrainous features in 40%, other types of chronic pain in 50%, and fatigue lasting >6 months in approximately 33%. These findings constitute a critical first step in changing the paradigm of our approach to FGID as a broader systemic disorder, not one limited to the gastrointestinal tract.