Axonal degeneration is a pivotal pathological event in most CNS and PNS diseases, but the molecular mechanisms that control this process remain unclear. Expression of the Wallerian degeneration slow (WldS) transgene robustly delays axon degeneration in various injury models and attenuate disease progression in many neurodegenerative conditions, indicating a common mechanism of axonal self-destruction in traumatic injuries and chronic degenerative events. In this thesis, I examined the mechanism of WldS axon protection as a window to understand the molecular events that orchestrate this axonal self-destruction program. In the first part of my thesis, I demonstrated that continuous, local WldS enzymatic activity in the axon, independent of nuclear gene transcription, is required to confer axonal protection. Furthermore, I showed that injured axons are not immediately committed to degeneration, but rather there is a critical period of 4-5hrs after injury in which the course of degeneration can be reversed. The presence of this latency period before the injured axons irreversibly commit to degeneration suggest that axonal degeneration can be attenuated or halted altogether even long after an injury has occurred. In the second part of the thesis, I investigated the signaling events and mechanisms that are responsible for translating WldS activity into axonal protection. I showed that NAD+, a metabolite of WldS enzymatic activity and a known redox cofactor in the mitochondria, is sufficient and specific to confer WldS-like axon protection. However, WldS axonal protection does not require the axonal mitochondria or involve changes in the bioenergy levels of the axon. I further demonstrated that independently increasing expression of Ca2+ buffering proteins in subcellular compartments is sufficient to delay axonal degeneration, suggesting that enhancement of Ca2+ buffering capacity in axonal subcellular compartments may be one mechanism by which WldS activity or NAD+ confers axonal protection. Finally, comparing the metabolomics profile of WT vs. WldS neurons reveals candidates in mediating NAD+ dependent regulation of intra-axonal Ca2+, and presents potential therapeutic targets to delay axon degeneration. In the third part of my thesis, I investigated the relationship between developmental axonal outgrowth, synaptic targeting and axon regeneration. Using retinal ganglion cells (RGCs) as a model system, I profiled the developmental expression of RGC genes from early embryonic to early postnatal development, a period that was previously shown to trigger a genetic switch to significantly slow the axonal growth rate. In particular, I showed that cyp1b1, a gene implicated in congenital glaucoma, is a potent source of retinoic acid during early RGC development and enhances RGC survival by sustaining retinoic acid production. In addition, several other genes from the expression profiling have been found by others to be involved in axonal regeneration after injury. Together, the findings provide a rich database for understanding the molecular signatures that control the development of retinal ganglion cells, and help uncover genetic factors that regulate axonal growth, targeting and regeneration.