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Background: The aim was to evaluate and validate a bowel disease questionnaire in patients attending an out-patient gastroenterology clinic in Greece., Methods: This was a prospective study. Diagnosis was based on detailed clinical and laboratory evaluation. The questionnaire was tested on a pilot group of patients. Interviewer-administration technique was used. One-hundred-and-forty consecutive patients attending the out-patient clinic for the first time and fifty healthy controls selected randomly participated in the study. Reliability (kappa statistics) and validity of the questionnaire were tested. We used logistic regression models and binary recursive partitioning for assessing distinguishing ability among irritable bowel syndrome (IBS), functional dyspepsia and organic disease patients., Results: Mean time for questionnaire completion was 18 min. In test-retest procedure a good agreement was obtained (kappa statistics 0.82). There were 55 patients diagnosed as having IBS, 18 with functional dyspepsia (Rome I criteria), 38 with organic disease. Location of pain was a significant distinguishing factor, patients with functional dyspepsia having no lower abdominal pain (p < 0.001). Significant factors distinguishing between IBS and functional dyspepsia were relief of pain by either antacids or defecation (19% vs 71% and 66% vs 0% respectively). Awakening from pain at night was also a factor distinguishing between IBS and organic disease groups (26% vs 61%, p < 0.01)., Conclusions: This questionnaire for functional bowel disease is a valid and reliable instrument that can distinguish satisfactorily between organic and functional disease in an out-patient setting.