This population based study compared the prevalence, nature and management of epilepsy between primary school children in mainstream education and those attending a special educational placement (children with special needs). The overall prevalence of epilepsy was 4.3/1000, but was 30 times higher in children with special needs, many of whom also had severe physical disabilities. Seizure types and the proportion of subjects with multiple seizures were similar in mainstream children and those with special needs. Epilepsy syndromes were identified in 74% of children. Although seizures were better controlled in children at mainstream school, 44% of these children did not have well controlled seizures. Children with epilepsy are an educationally vulnerable group and both education and health staff need to be aware of the additional support that many of these children require in all types of primary educational settings.