The past several years have seen an increased appreciation of the potential role of the endocrine system in the recovery process following surgery for congenital heart disease. Many of the hormonal changes following cardiac surgery are adaptive and necessary, whereas activation of proinflammatory cytokine and chemokine responses and some of the metabolic changes following surgery are likely mediators leading to detrimental outcomes. Additionally, other hormonal perturbations may contribute to adverse outcomes. This review examines the pain and the stress response, thyroid function and hyperglycemia following cardiopulmonary bypass (CPB), and the potential role of corticosteroids in the pediatric cardiac critical care unit.