Congenital central hypoventilation syndrome (CCHS) is characterized by a failure of the automatic control of breathing during sleep, and is caused by the dominant PHOX2B mutation. PHOX2B encodes a highly conserved homeobox transcription factor with two short polyalanine tracts. More than 90% of patients carry polyalanine expansion mutations (PARM) in the polyalanine tract of 20 residues and less than 10% of the patients have missense, nonsense, or frameshift mutations(non-PARM). Approximately 25% of the patients with PARM inherited the mutation from asymptomatic parents with somatic mosaicism or few affected parents. Molecular analysis can provide the definite diagnosis and clinically useful information. Model mouse experiments and MRI study of the patients will contribute to understanding the pathogenesis and development of new treatment strategy.