Congenital central hypoventilation syndrome (CCHS) is a rare disorder defined by a failure in autonomic control of breathing secondary to mutations of the PHOX2B gene. Affected individuals demonstrate absent or diminished physiologic response to hypercapnia and hypoxia that is most severe during sleep as well as multi-system dysregulation of autonomic functions. Areas covered: In this review, we will discuss how evaluation of the disease-defining PHOX2B gene aids diagnosis and helps prognosticate disease severity, review disease physiology, describe clinical presentation and various aspects of autonomic nervous system dysregulation, review ventilatory strategies, and highlight current challenges in the care of these complex patients. Expert commentary: CCHS is a rare disorder that requires a high degree of vigilance. PHOX2B mutation is essential for diagnosis and also helps direct disease management. There is currently no pharmacologic treatment proven effective in improving disease-related hypoventilation and care is focused on providing adequate ventilatory support and managing autonomic dysfunction.