The etiopathogenesis of eating disorders (EDs) is complex and still not well understood. Biological, psychological and environmental factors (e.g. childhood abuse) have all been considered to be involved in the onset and the persistence of EDs. The hypothalamic-pituitary-adrenal (HPA) axis is a relevant biological factor capable of influencing the onset and the course of EDs and not many information are available about the impact of a Cognitive Behavioral Therapy (CBT) on cortisol changes in EDs. The HPA-axis functioning has been evaluated before and after CBT in a group of patients with Anorexia Nervosa (n = 34) and Bulimia Nervosa (n = 35) according to the presence/absence of a history of sexual/physical abuse. At baseline, only patients reporting childhood abuse showed lower morning cortisol levels as compared with other patients of the same diagnostic group and Healthy Controls. After CBT, a variation of cortisol levels has been found only in patients without abuse, suggesting a role of childhood adversities in the persistence of HPA-axis alterations in Eating Disorders.