Following Spinal Cord Injury the sensorimotor and limbic system immediately undergo progressive neurodegeneration (atrophy). Next to the focal grey and white matter atrophy, localized CSF and ventricular volume changes may provide additional biomarkers for brain atrophy. We therefore aimed to track brain atrophy by means of CSF volume changes and ventricular enlargements over two years following SCI. Our finding showed an increase of local CSF volume as well as ventricles enlargement in patients over time. The CSF volume which is normally used as a biomarker of general atrophy, showed also sensitivity to local degenerative changes in SCI.