Little information on functional status and well-being is available in patients with functional gastrointestinal disease. We aimed to evaluate whether quality of life is poorer in patients with functional dyspepsia. A consecutive sample of 73 patients with functional dyspepsia completed a validated questionnaire prior to endoscopy. Organic disease controls comprised 658 outpatients attending endoscopy. Quality of life was measured using the validated Medical Outcomes Survey (which assessed physical, role, and social functioning; mental health; health perception; and any bodily pain) and the Brief Symptom Inventory (for current anxiety and depression); additional specific gastrointestinal items were also included. A stepwise logistic regression analysis was used to assess the association between diagnostic group and the quality of life measures, adjusting for potential confounders. Patients who reported more interruptions in their daily activities due to abdominal pain and who had fewer limitations of physical functioning were more likely to have functional dyspepsia (vs other disease, P < 0.01). Mental health, social functioning, and health perception also tended to be poorer in functional dyspepsia. We conclude that quality of life may be more impaired in patients with functional dyspepsia than in patients with other conditions who present for upper endoscopy.