An outbreak of enterovirus 71 (EV71) infection occurred in Taiwan in 1998. The clinical spectrums and laboratory findings for 97 patients with virus culture-proven EV71 infections were analyzed. Eighty-seven percent of the patients were younger than age 5 years. Hand-foot-and-mouth syndrome occurred in 79% of the children and central nervous system (CNS) involvement in 35%, including nine fatal cases. The predominant neurological presentations were myoclonus (68%), vomiting (53%), and ataxia (35%). Brain stem encephalitis was the cardinal feature of EV71 CNS involvement during this outbreak. Magnetic resonance imaging and pathological findings illustrated that the midbrain, pons, and medulla were the target areas. EV71 brain stem encephalitis can present either with cerebellar signs and an initially mild, reversible course or with overwhelming neurogenic shock and neurogenic pulmonary edema (NPE) resulting in a fatal outcome. Brain stem encephalitis that progressed abruptly to neurogenic shock and NPE was indicative of poor prognosis in this epidemic. Early aggressive treatment and close monitoring of the neurological signs are mandatory to improve the chance of survival.