Although functional gastrointestinal symptoms are seen frequently by internists and are the commonest reason for patients to be referred to gastroenterologists, no validated self-report questionnaire is available for their diagnosis. To differentiate among non-ulcer dyspepsia, the irritable bowel syndrome, organic gastrointestinal disease, and health, we developed a self-report questionnaire. Our bowel disease questionnaire, which evaluated 46 symptom-related items was completed prospectively by 361 subjects before their clinical evaluation as outpatients. Of these subjects, 115 were categorized ultimately as having functional bowel disease (non-ulcer dyspepsia or the irritable bowel syndrome), 101 were categorized ultimately as having organic gastrointestinal disease, and 145 were healthy persons having routine periodic examinations for whom no additional diagnoses were made. All diagnoses were based on independent clinical evaluations, not on the patients' responses to the questionnaire. The bowel disease questionnaire was acceptable and easily completed; it elicited symptoms in a highly reliable manner and was shown to be a valid measure of functional bowel complaints. Our questionnaire discriminated non-ulcer dyspepsia from irritable bowel syndrome with a sensitivity of 75% and a specificity of 72%, and it discriminated functional bowel disease from organic disease and health with sensitivities of 85% and 83%, and specificities of 60% and 76%, respectively. We believe that this questionnaire is an additional and useful diagnostic tool for identifying patients with functional gastrointestinal symptoms.