Axons are essential, vulnerable and often irreplaceable so it is essential to understand how they are lost in neurodegenerative disease. Recent data link the mechanism of injury-induced Wallerian degeneration to that of axon death in CNS and PNS disease. The neuroprotective gene WldS delays Wallerian degeneration, CNS axonal dystrophy, ‘;dying-back’ pathology and to a lesser extent synapse loss, despite the different causes and morphologies of degeneration. These findings validate Wallerian degeneration as a model to understand and prevent mechanisms of axon and synapse loss in neurodegenerative disorders. The existence of a gene that alters Wallerian degeneration suggests it is a regulated program of axon death normally held back by axonal inhibitors, similar in principle to apoptosis. The WldS protein and proteasome inhibitor experiments implicate the ubiquitin proteasome system (UPS) in Wallerian degeneration. However, the site of UPS involvement and the molecular events remain unclear because the UPS is highly compartmentalized in neurons, affecting complex and sometimes conflicting processes in nuclei, axons, growth cones and synapses. Proteasome inhibitors are blunt tools for studying such a complex system and they are also particularly toxic to axons and alter synapse function. In contrast, WldS acts on a specific step, leaving mice healthy with normal development and behavior. This also makes it an attractive drug target. We need to understand which UPS step is blocked in which neuronal compartment, and to define the pathway in order to develop new strategies to block axon pathology.