Chronic abdominal pain (CAP) is a common complaint encountered in pediatric clinics and a great concern for patients and their caretakers as well as health care professionals. A constant challenge is detecting individuals with organic diseases or psychosomatic disorders from the majority of patients who have a functional disorder including functional dyspepsia, irritable bowel syndrome, functional abdominal pain, and abdominal migraine. Beginning with a detailed history and physical examination, physicians must determine a differential diagnosis of CAP by applying the symptom-based Rome III criteria to positively identify a functional disorder. These findings should then be further analyzed based on diagnostic clues and red flags that indicate the presence of specific organic diseases and/or the need for further testing. Once a functional diagnosis has been made or an organic disease is suspected, physicians can initiate an empiric therapeutic trial. Since psychological distress accompanies both organic and non-organic abdominal pain in children, a cooperative diagnostic approach involving pediatricians and psychiatrists is recommended.