The protein profiles in the cerebrospinal fluid of 10 patients with multiple sclerosis (MS), 10 patients with neuromyelitis optica (NMO), 8 inflammatory disease control patients, and 4 noninflammatory disease control patients were screened by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. Peaks of 12.5 kDa were significantly lower in multiple sclerosis, NMO, and inflammatory disease control patients than in noninflammatory disease control patients, and 13.4 kDa peaks were higher in NMO than in inflammatory disease control patients. Further analyses demonstrated that both peaks were cystatin C. Enzyme-linked immunosorbent assay showed that the cystatin C levels tended to be lower in multiple sclerosis and NMO. Alterations of cystatin C may relate to the pathogeneses of demyelinating diseases.