A 21-year-old healthy female suffered from an upper respiratory tract infection and 2 days later developed diplopia, unsteady gait, dysarthria and a profound disturbance of consciousness with rapid development of coma. Brain MRI and Tc99m brain perfusion SPECT, EEG, neurophysiological tests and CSF analysis results were unspecific. The detection of serum anti-GQ1b IgG autoantibodies at high titre led to the diagnosis of Bickerstaff's brainstem encephalitis (BBE). Clinical symptoms resolved after treatment with plasma exchange and the outcome was good. Brain MRI was normal, and Tc99m brain perfusion SPECT demonstrated hypoperfusion of the whole cerebral hemispheres and basal ganglia with relative sparing of the thalami and the brainstem. Similar to brain MRI, the sensitivity of Tc99m brain perfusion SPECT in detecting brainstem lesions in typical BBE patients seems to be low.