OBJECTIVE To study the clinical features and treatment of serious brainstem encephalitis caused by enterovirus 71 (EV71) infection. METHODS The clinical data of 32 hospitalized children with serious brainstem encephalitis caused by EV71 infection between May and December 2008 were retrospectively reviewed. RESULTS The children whose age was younger than 3 years old accounted for 88% (22 cases). Fever(>38.5 degrees centigrade)lasting at least 3 days, frequent vomiting and limb twitch were presented as the main manifestations in the 32 children. Cyanosis, tachypnea, tachycardia and cold extremities were observed, and pulmonary edema or even pulmonary hemorrhage occurred in 8 children 3 to 4 days after the onset. The 32 children received a medical treatment: reduction of intracranial pressure with mannitol or frusemide, inhibition of inflammation reactivity with gamma globulin and methylprednisolone, and improvement of cardiac function and pulmonary edema with innotropic agents, fluid restriction and positive mechanical ventilation. CONCLUSIONS Vegetative nerve functional disturbance is the main clinical feature of brainstem encephalitis caused by EV71 infection in children. An early identification and treatment of pulmonary edema or hemorrhage is of great importance.