The use of genetically modified mice to study axon regeneration after spinal cord injury has served as a useful in vivo model for both loss-of-function and gain-of-function analysis of candidate proteins. This review discusses the impact of genetically modified mice on axon regeneration after spinal cord injury in the context of axon growth inhibition by myelin, the glial scar, and chemorepellent molecules. We also discuss the use of mice which transgenically express fluorescent proteins in specific axons for increasing our understanding of how spinal cord axons behave after injury.