Axonal damage is considered the major cause of irreversible disability in multiple sclerosis (MS). Which mechanisms underlie the damage and whether this is secondary to myelin damage remains to be clarified. Recently, we have demonstrated that autoimmunity to the axonal/neuronal cytoskeletal protein neurofilament light (NF-L) induces axonal damage and neurological disease including spasticity - a common feature of MS. To examine the relationship between axonal damage and demyelination we have characterized the detailed neuropathology of NF-L-induced disease in Biozzi mice compared to classical experimental autoimmune encephalomyelitis (EAE) induced with myelin oligodendrocyte glycoprotein (MOG). In NF-L-induced neurological disease the lesions were predominantly located in the dorsal column displaying extensive axonal degeneration, but were also abundant in the gray matter. In contrast, lesions in MOG-EAE were restricted to the lateral and ventral columns and displayed less axonal damage and little gray matter involvement. The differential lesion location was confirmed by quantitation of leukocyte subsets. In both diseases myelin damage was a common feature although the numerous empty myelin sheaths in NF-L-disease indicative of axonal damage suggest that myelin damage was a secondary event. In summary, autoimmunity to NF-L induces a distinct lesion topology, axonal damage and gray matter lesions supporting the notion that axonal loss and gray matter pathology can be the direct consequence of a primary autoimmune attack against axonal antigens such as NF-L rather than merely a secondary event to myelin damage.