Understanding the mechanisms driving neuronal degeneration and axonal damage is key to the development of relevant therapies for neurological diseases. In the past several decades a gradual awareness of the different mechanisms involved in neurodegenerative disease such as Alzheimer's' disease, multiple sclerosis, brain trauma, amyotrophic lateral sclerosis and Parkinson's disease has emerged. Here we first discuss how infections, malignancies and trauma trigger autoimmunity to neurons and axons. Next we review the different mechanisms by which antibodies and T cells induce dysfunction and damage neurons and axons, or conversely, how such pathways could be beneficial in neurodegenerative disorders. Clarification of the different autoimmune mechanisms underlying neurodegeneration will be useful to develop novel therapeutic approaches.