The nosological position of Bickerstaff's brain stem encephalitis (BBE) has yet to be established, and its etiology is not clear. Because anti-GQ1b antibody frequently occurs in patients with Fisher's syndrome (FS) and there are clinical similarities between FS and BBE, we investigated anti-ganglioside antibodies in sera from 3 BBE patients who had transient long tract signs in addition to acute ophthalmoplegia and cerebellar-like ataxia in order to clarify the etiology and nosological position of BBE. High IgG anti-GQ1b antibody titers were present in all 3 sera samples but decreased with the clinical course of the illness. In contrast, no anti-GQ1b antibody was found in sera from patients with other neurologic diseases which were able to produce transient brain stem disturbance: multiple sclerosis, neuro-Behçet's disease, brain stem infarction, herpes simplex virus encephalitis, and Wernicke's encephalopathy. The finding that BBE and FS shared common autoantibody suggests that autoimmune mechanism common to FS is likely in BBE, and that both conditions represent a distinct disease with a wide spectrum of symptoms that include ophthalmoplegia and ataxia.