Few studies have quantified the change in cortical white matter tracts following chronic spinal cord injury in a pediatric population. Additionally, no work has been done to compare chronic SCI subjects with different American Spinal Injury Association Impairment (AIS) scale classifications. We hypothesized that these cortical changes can be detected using tract-based spatial statistics (TBSS). Our efforts revealed that significant changes in fractional anisotropy occur in several motor and sensory related regions. We conclude that TBSS can be effectively used to identify alterations in brain microstructure in a chronic pediatric spinal cord injury population.