We analyzed the prevalence of severely hypointense lesions on T1-weighted MRI in the brainstem, spinal cord, and optic nerve from 65 patients with MS. About half of 1,274 supratentorial lesions were classified as severely hypointense. Severe hypointensity was not seen in the optic nerve and spinal cord, and in only one of 168 chronic brainstem lesions. Tissue destruction in the brainstem, spinal cord, and optic nerve of MS patients does not usually result in severely hypointense lesions.