Glial fibrillary acidic protein (GFAP) is the major structural protein of the intermediate filaments found in glial cells. Increased levels in the cerebrospinal fluid (CSF) have been found to indicate gliosis. Neurofilament (NFL) is a structural element of neurons, mainly found in large myelinated axons. Its presence in the CSF has been suggested to reflect destruction of axons. The aim of this study was to see if GFAP and NFL in the CSF of children with neurological disabilities and an abnormal signal on magnetic resonance imaging (MRI) of the cerebral white matter could be used to clarify the underlying neuropathology. The potential of GFAP and NFL to differentiate a progressive disease from a stationary disorder was investigated, as was the correlation with disability and clinical findings. CSF from 26 children, eleven with progressive and 15 with non-progressive disorders, was analysed. GFAP was increased in all, interpreted to reflect gliosis. NFL was elevated in seven and considered to indicate ongoing neuroaxonal damage as all but one patient were found to have a progressive disease. GFAP did not differentiate between progressive and non-progressive disorders, although low levels were found in stationary and high levels in progressive disorders. The severity of the disability correlated with the NFL levels, but not with the concentration of GFAP.