The aim of this study has been to establish the incidence rate (IR) and main characteristics of childhood epilepsy in Estonia. A population-based prospective study was performed from January 1st 1995 to December 31st 1997 in seven counties (population of children 161202). Only cases occurring in the age range of 1 month to 19 years with active epilepsy were included. Two hundred and sixteen cases met the study criteria. The total age-adjusted IR was 45/100000. The IR was the highest, 73/100000, in the age group from 1 month to 4 years. The IR declined markedly after the age of 15 years. Primarily generalized seizures demonstrated a higher IR, 25/100000, than partial seizures, the IR of which was 20/100000. The IR of symptomatic epileptic syndromes was 16/100000, that of cryptogenic, 15.5/100000 and that of idiopathic, 13/100000. The cumulative incidence of epilepsy through age 19 was 0.13%. A family history of epilepsy was present in 13.9% of cases. In 40.7% of cases the cause of epilepsy was identified. Adverse perinatal events were the most frequent etiological factors: in 25%, IR 11/100000. In 103 cases (47.6%) additional medical problems were disclosed. Strong negative univariate association was noted between partial seizures and idiopathic etiology (OR 0.37, 95%CI 0.18, 0.72; P = 0.002) and between partial seizures and motor disability (OR 0.43, 95%CI 0.24, 0.78; P = 0.003). The incidence of childhood epilepsy in Estonia was comparable with developed countries. Generalized seizures predominated. Perinatal factors were the main causes. The idiopathic etiology and motor disability of cryptogenic and symptomatic cases were associated with generalized seizures.