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Abdominal pain and bowel habits alterations are common symptoms in the general population. The investigation to differentiate organic from functional bowel disorders represents a considerable burden both for patients and public health service. The selection of patients who should undergo endoscopic and/or radiological procedures is one of the key points of the diagnostic process, which should avoid the abuse of invasive and expensive tests as well as the underestimation of potentially harmful diseases. Over the coming years,clinicians and researchers will be challenged to develop strategies to increase the patient's compliance and to reduce the economic and social costs of the intestinal diseases.