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The necessity of lumbar puncture for the differentiation of central nervous system infection in children with febrile status epilepticus (FSE) remains controversial. The aim of the present study is to investigate the diagnostic necessity of lumbar puncture for children with FSE after the introduction of bacterial conjugate vaccines into the infant immunization program.Our retrospective cohort study was performed in children 6 to 60 months of age who were admitted to the pediatric ward at Kitakyushu General Hospital from January 1, 2011, to December 31, 2015, for seizures with fever. Of these patients, we compared the clinical characteristics between the patients initially diagnosed as having FSE and complex febrile seizures excluding FSE (non-FSE).Of the eligible 333 children, 98 and 235 children were classified into FSE and non-FSE groups, respectively. The proportion of the children who underwent lumbar puncture in FSE group was significantly higher than that in non-FSE group (P < 0.0001). On the other hand, no significant difference in the proportion of the patients with abnormal cerebrospinal fluid findings was seen between the 2 groups. There was no patient with bacterial meningitis. The proportion of patients with encephalitis/encephalopathy in FSE group (n = 7, 7.1%) was significantly higher than that in non-FSE group (n = 0, P = 0.0003). However, only 1 of 6 patients with encephalitis/encephalopathy who underwent lumber puncture showed pleocytosis in cerebrospinal fluid.Routine lumbar puncture for the differentiation of severe central nervous system infection cannot be recommended in children with FSE.