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Once the presumptive diagnosis of celiac disease is made then treatment may be commenced. It is important that the patient does not start to restrict their diet until each of the steps including the biopsy have been completed. Once confirmed, the responsibility for directing the management of the patient lies with the physician.

The treatment starts with an explanation of the condition and its cause. It is important that the patient understands that this is a chronic inflammatory condition of the gut and not a simple food allergy, that it is permanent eventhough the intestine will heal, and that the central and indeed only treatment at present is a gluten-free diet for life. The clinician should expect shock and even a fully expressed grief reaction on the part of the patient. Disbelief that something as basic to the Western diet as wheat is responsible is common. Some patients are overwhelmed both by the realization of having a chronic illness and others by relief that an explanation for their suffering has been found. The tone that the physician sets is crucial to the patient's success. A positive and upbeat though serious demeanor on the part of the doctor is appropriate, as most patients will do very well so long as they stick to the diet. Probably the most important thing that the doctor can do beyond diagnosis is to refer the patient for professional dietary advice that is up to date on how to achieve a gluten-free life style.

Patients should be encouraged to join both local and national support groups as an essential adjunct to management. The feeling of isolation so common in newly diagnosed patients in the past can be quickly dispelled by participation in an active support group.

It is important to identify and to correct deficiencies with nutritional supplementation. Deficiencies of the fat-soluble vitamins (D, E, A, and K), iron, folate, B12, and even zinc or selenium are common. Baseline bone mineral density should be measured, as osteoporosis and osteomalacia are common.

Occasionally, intensive nutritional support and fluid replacement may be needed in very ill patients. Coexisting malignancy/autoimmune disease should be considered especially in elderly or ill patients.

Follow-up of patients to ensure response to gluten-free diet and compliance is crucial to ensure long-term compliance as well as detecting potential complications of the disease. Screening of at-risk family members should be considered.

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