OBJECTIVE: The possible effect of obesity in the outcome of treated children with abdominal pain-related functional gastrointestinal disorders (FGIDs) has not yet been studied. We hypothesized that obesity is associated with a poor long-term prognosis in children with FGIDs. STUDY DESIGN: Prospective cohort study in an outpatient clinic-based sample of patients diagnosed with abdominal pain-related FGIDs. Principal outcome measured was persistence of pain at long-term follow-up (12-15 months). Frequency of pain, intensity of pain, school absenteeism and disruption of daily activities were compared between obese and non-obese subjects. RESULTS: The group mean age was 13.27+/-3.84 years, distribution of diagnosis was 32% (functional abdominal pain), 42.5% (irritable bowel syndrome) and 25.5% (functional dyspepsia). Overall, 20.2% of patients were obese. A total of 116 patients (61.7%) reported abdominal pain and 72 (38.3%) were asymptomatic at long-term follow-up. Obese patients were more likely to have abdominal pain (P<0.0001), higher intensity of pain (P=0.0002), higher frequency of pain (P=0.0032), school absenteeism (P<0.0001) and disruption of daily activities (P<0.0001) at follow-up than non-obese patients. CONCLUSION: Obesity is associated with poor outcome and disability at long-term follow-up in children with abdominal pain-related FGIDs. Our novel findings could have important implications in the prognosis and management of FGIDs.