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The purpose of this study was to evaluate the clinical characteristics of nervous system damage caused by enterovirus 71 (EV71) infection in pediatric patients.Clinical data and outcomes were retrospectively analyzed for 134 cases of laboratory confirmed pediatric EV71 infection admitted to the Children’s Hospital of Chongqing Medical University from January to December 2013.EV71 infection was significantly more common in patients 1–4 years of age, in males and during the months of April–July. Fifty-six cases complicated by hand, foot and mouth disease were diagnosed. Fever was the most common symptom (128 of 134 patients) and lasted on average 5.3 ± 2.1 days. The most common neurologic complication was aseptic meningitis (n = 74), followed by brain stem encephalitis (n = 24), acute flaccid paralysis (AFP; n = 20), acute parencephalitis (n = 12) and encephalomyelitis (n = 4). Each was characterized by a unique profile of clinical symptoms. Damage to the pons and medulla oblongata was apparent in 28 brain magnetic resonance images. Lesions associated with AFP were concentrated in the cervical spinal cord and thoracic 8. The anterior root of the spinal anterior horn was a specific lesion. Fourteen of the AFP patients had unilateral or bilateral femoral nerve involvement. None of the patients died, and in 132 of 134 patients, follow-up visits showed that their physical and neuropsychologic abilities had returned to normal.Most children infected with EV71 have a good prognosis if they are diagnosed early and receive proper supportive treatment.