This chapter focuses on classic congenital central hypoventilation syndrome (CCHS) cases in which symptoms appear early in life. The principal issues in CCHS are to determine what brain structures are damaged in CCHS to cause the loss of CO2 and O2 sensitivity, disturbances in autonomic function, and other affective and cognitive deficits. Among the processes affected in CCHS appears to be the integrity of multiple neurotransmitter systems. Structural and functional magnetic resonance imaging (MRI) procedures provide a valuable means to assess gray and white matter injury and impaired brain function in the syndrome, and, in the same fashion as numerous other disease processes, the descriptions have the potential to reveal normal mechanisms for serving breathing and autonomic functions. Injury in cognitive and memory regulatory areas has also been revealed. As MRI technology improves, further differentiation of the nature of injury, especially finer discrimination of fiber injury, will be possible.