Substantial progress has been made towards understanding the molecular basis for limited endogenous central nervous system (CNS) axonal growth after injuries such as spinal cord trauma. Realization of the potential benefit of therapeutic interventions requires methods to assess axonal growth and functional reorganization over time after neurological damage. Here, we discuss the technical challenges of analyzing and interpreting the effects of various interventions on CNS repair, specifically in the context of spinal cord injury. Evolving technologies such as functional magnetic resonance imaging and other non-invasive imaging techniques will be reviewed. These technologies should revolutionize our ability to track changes in both CNS structure and function.