To clarify the mechanism of brain and spinal cord impairment in Rett syndrome (RS), we measured the cerebrospinal fluid (CSF) levels of substance P in 20 patients with RS including 16 childhood patients and 4 adult patients. Findings were compared with those obtained in age-matched controls and diseased controls. The CSF level of substance P was significantly lower in patients with RS compared with controls. The alteration in the CSF level of substance P may be related to the neurological impairment, especially autonomic dysfunction, and neuropathological involvement of dorsal root ganglia and peripheral nerve observed in RS.