Patients with chronic fatigue syndrome (CFS) or fibromyalgia, two prevalent and poorly understood disorders, experience symptoms of fatigue and myalgias that are reminiscent of those experienced by patients with adrenal insufficiency. This overlap in symptoms has prompted investigations into the functioning of the hypothalamic-pituitary-adrenal (HPA) axis in these disorders. In general, studies in patients with CFS or fibromyalgia have shown either normal HPA axis activity or mild impairment, without frank glucocorticoid deficiency. Impairments in HPA axis activity, when present, appear to be caused by alterations in hypothalamic, pituitary activity resulting in decreased ACTH levels in response to stressors. The specifics of these alterations may vary between CFS and fibromyalgia. Although glucocorticoids are not beneficial in fibromyalgia, approximately one-third of CFS patients show a decrease in fatigue with glue cocorticoid therapy. However, the rational for this response is unclear and cannot be predicted by baseline HPA testing. Glucocorticoid therapy is not recommended. In addition to changes in HPA axis activity, patients with fibromyalgia or CFS may have alterations in other hormone systems and in autonomic nervous system function. Although the changes in each system are subtle, the combination in one individual of several mild impairments may result in an altered response to stressors that potentially could contribute to the pathophysiology of CFS and fibromyalgia. If so, therapies that improve neuroendocrine and autonomic nervous system responses to stress may be beneficial.