Multiple Sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS). MS is characterized by demyelinating lesions that occur in different regions of the CNS at different times. The cause of the inflammatory lesion in MS remains uncertain and the antigenic targets are unknown. Although antibodies specific for immune proteins expressed in myelin, axons and the nodes of Ranvier have been shown to occur in MS and may be salient to the disease process, none have yet been consistently associated with the pathogenesis of the disease. Given that the principal correlate of brain atrophy in pathology studies of MS is the loss of neurons and that brain atrophy correlates with clinical outcomes, this study was designed to determine whether neuronal antibodies are found in MS and whether they are associated with clinical outcome measures and disease phenotypes. Serum from 79 patients with MS, 60 patients with other inflammatory neurological disease (OIND), 15 non-inflammatory neurological controls (OND) and 61 healthy blood donors were analysed using indirect immunofluorescence on rat brain and spinal cord tissues. High titre neuronal antibodies were more prevalent in MS patients (19%) than OIND (16.7%, OND (0%) and healthy controls (6.6%). Neuronal antibodies in MS were identified against the cell soma, cell cytostructure, dendrites and synapses and the neuropil. The most frequently identified antibody in MS was directed against interneurons. Neuronal antibodies in MS did not correlate with disease duration or disability scores. However, neuronal antibodies were only found in cerebral-predominant (rather than spinal predominant) forms of MS and were not detected in the similar but distinct demyelinating disease, Neuromyelitis Optica. Taken together these findings imply that whilst neuronal antibodies are not specific for MS, they may have a role in inflammatory progression of the disease, in contradistinction to NMO which is very rarely progressive in form.