Background: Previous studies in special schools have shown a high prevalence of epilepsy, which is strongly associated with cerebral palsy and severe mental retardation. The conditions regulating school placement have also been described in those studies. In the City of Buenos Aires, information is known only for mainstream schools. Objective: To determine the prevalence and characteristics of epilepsy in special schools and to compare results with common primary education settings. Design and Methods: A cross-sectional study was carried out in special schools in the City of Buenos Aires, by adopting the same definitions, diagnostic criteria and questionnaire as those used in a previous study in the common primary school population. Responses from 1,682 children, aged 6–16 years, residing in the City of Buenos Aires, with mental retardation, visual or hearing impairment, psychiatric disorders and motor disabilities were analyzed. Results: A total of 121 children with epilepsy were detected. Lifetime prevalence was 71.9‰ and active prevalence was 64.8‰ (22–25 times greater than rates in mainstream schools). Prevalence was highest in girls and generalized seizures prevailed over other seizure types. Ninety-two percent of cases received antiepileptic drugs, 57.9% as a single drug treatment and 85.1% in adequate doses. Only 56% of the children with a diagnosis of epilepsy proved to be true-positive cases, and almost 40% received antiepileptic drugs for nonepileptic disorders. Malformations/degenerative disease were the most common etiology. Conclusions: Special schools contain clusters of children with epilepsy as a comorbid condition. False high frequency is due to misdiagnoses and unnecessary treatments. These schools are an important target for educational interventions.