Patients with chronic medical complications associated with an eating disorder (ED) often elicit negative counter-transference from medical care providers. From a clinical standpoint, the primary area of the brain affected by EDs, especially with weight loss, is the hypothalamus, with important influence on the endocrine regulatory function. Amenorrhea related to decreased hypothalamic function is one of the most clinically relevant chronic medical complications of EDs. It is a diagnostic feature of anorexia nervosa (AN) and is associated with both infertility and low levels of sex steroids. The primary focus of treatment for adolescent patients with EDs who experience menstrual irregularities and amenorrhoea should be weight recovery and normalization of eating habits. Although chronic dysfunctional weight control habits practised by children and adolescents with EDs have recognized effects on all tissues, the primary foci with respect to chronic medical complications are the heart, brain, gonads and bones.