A case of remitting-relapsing Bickerstaff encephalitis is reported. The article focuses on its imaging findings and their significance when a clinical differentiation between Bickerstaff encephalitis and Miller-Fisher syndrome is attempted. Signs and symptoms may occasionally overlap. However, because Miller-Fisher syndrome is related to the peripheral nervous system and Bickerstaff encephalitis is a central disease, the recognition of brain stem hypointense lesions on T1-weighted images, which are hyperintense on T2-weighted sequences, could be a reliable tool when the clinical diagnosis is unclear.