We followed the presence of autoantibodies to neurofilaments (NF) in the sera of patients with acute tick-borne encephalitis (TBE), chronic TBE, amyotrophic lateral sclerosis (ALS), and other diseases of CNS. The diagnosis was made according to clinical signs and based on virus neutralizing antibodies. Autoantibodies to NF were found in the majority of chronic TBE patients during disease progression, but were neither present in acute TBE nor in chronic TBE cases during the stabilization phase. Autoantibodies to NF found in a patient with acute TBE showed subsequent progression to a prolonged course. The data are discussed in order to assess the mechanisms of the chronic TBE process and its role in impairing the slow axonal transport.