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"Functional" illness refers to illness or symptoms "that cannot be explained on a structural, physiologic, or biochemical basis." ( Kliegman: Nelson Textbook of Pediatrics, 18th ed.) If your child is diagnosed with a functional illness, this does NOT mean that the doctor thinks your child's symptoms are unreal. Perhaps another way to express what is going on would be to term it a DYSfunctional illness, in the sense that an organ system (most often the gastrointestinal system) does not function properly. "Not functioning properly" could involve pain or cramps, irregular bouts of unexplained constipation or diarrhea, nausea or vomiting, etc.
Functional symptoms may be associated with stressful situations - "stress related illness." Whether or not this is the case, the patient has real and perhaps distressing symptoms for which there is no easy or obvious explanation, but the important thing is that the cause is not a serious illness.
Dealing with functional illness involves first ruling out organic causes. This does not mean that every test in the hospital has to be done. A thoughtful and complete history and physical examination is the first step, followed by a carefully selected set of laboratory tests and any indicated xray or other studies. When the organic causes of the symptoms have been ruled out, discussion can turn to managing the symptoms. This may involve medication, although medication is generally avoided; diet changes - for example, increasing dietary fiber is often very helpful for functional abdominal pain; stress management, because anyone under stress tends to notice more bodily aches and discomforts; or other approaches focusing on alleviating the interference with everyday life that the symptoms cause.