The present invention provides assays and kits for diagnosing idiopathic congenital central hypoventilation syndrome. The present assays and kits focus on the second polyalanine repeat of the PHOX2b gene or gene product, which is normally 20 residues in length. A polyalanine repeat 25 to 33 residues in length is strongly correlated with idiopathic congenital central hypoventilation syndrome.