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Primary care physicians in Japan are often unwilling to vaccinate children with neurological disorders. The aim of the present study was to determine the state of vaccination in children who are severely handicapped and/or have convulsive disorders, in order to increase the vaccination rate in this patient population.Six hundred and eighty pediatricians belonging to Osaka Shonika Ikai were asked to answer a questionnaire, and 359 doctors responded.Two hundred and thirty-four doctors consulted for febrile seizures (Fs), 190 for epilepsy and 145 for conditions affecting severely handicapped children, responded that they refused to vaccinate. The reasons for reluctance to vaccinate these children were short interval since the last seizure, including febrile (226 doctors) and epileptic (121 doctors) seizures. It was especially likely that a child with a past history of status epilepticus would be refused vaccination. Primary care doctors are very cautious about the indications for vaccination, especially the inoculation of live vaccines, because they often induce post-vaccination fever-associated convulsions. Intractable daily epileptic seizures was the most common reason for refusal to vaccinate severely handicapped children. Examples of inadequate decision-making as regards the indications for vaccination were: “need more than 6 months observation since last seizure whether Fs or epileptic”, “need EEG examination for Fs”, “contraindication because of low bodyweight and/or chronic wheezing in severely handicapped children”.There is a need to provide correct information about the adverse effects of vaccination and for greater cooperation between primary care doctors and pediatric neurologists.