Rett syndrome (RS) is a clinically defined disorder characterized by autistic behavior, and cognitive and motor skill loss early in life. We performed 1H-MRS of the brain in 3 cases of RS in comparison with in autism and controls. The older patient with RS demonstrated decreased N-acetylaspartate (NAA)/choline (Cho) and NAA/creatine (Cr) ratios when compared with the autism and control groups, whereas the younger patients did not demonstrate these decreased metabolite ratios. The Cho/Cr ratio did not differ among Rett syndrome, autism and controls. Since the clinical stage did not differ among the 3 cases of RS, it was suggested that NAA was decreased with increasing age and was not related with the clinical stage of RS. The NAA/Cho, NAA/Cr and Cho/Cr ratios did not differ between autism and controls. The present data suggest that there may be a secondary degenerative process of late onset in RS, which pathophysiologically differs from autism.