Long considered a rare and unique disorder of respiratory control, congenital central hypoventilation syndrome has recently been further distinguished as a disorder of autonomic regulation. Similarly, more recent evidence suggests that sudden infant death syndrome is also a disorder of autonomic regulation. Congenital central hypoventilation syndrome typically presents in the newborn period with alveolar hypoventilation, symptoms of autonomic dysregulation and, in a subset of cases, Hirschsprung disease or tumors of neural crest origin or both. Genetic investigation identified PHOX2B, a crucial gene during early autonomic development, as disease defining for congenital central hypoventilation syndrome. Although sudden infant death syndrome is most likely defined by complex multifactorial genetic and environmental interactions, it is also thought to result from central deficits in the control of breathing and autonomic regulation. The purpose of this article is to review the current understanding of these autonomic disorders and discuss the influence of this information on clinical practice and future research directions.