A 3.5-year follow-up study of cognition and behaviour in 42 children with newly diagnosed idiopathic or cryptogenic epilepsy ('epilepsy only') attending mainstream education and 30 healthy gender-matched classmate controls was carried out to identify differences between groups, to detect factors that contribute to the difference and its change over time, and to establish the proportion of poorly performing children. The neuropsychological battery covered the major domains of cognition, mental and motor speed and academic language skills. Children were tested at the time of diagnosis (before any anti-epileptic drug treatment started) and 3, 12 and approximately 42 months later. Parents and teachers completed behaviour checklists, for which the scoring was adapted to prevent any influence of epilepsy-related ambiguity. Based on parental interviews at the time of diagnosis, children with epilepsy were categorized as having longstanding behavioural and/or learning problems, as belonging to a troubled family, as being exposed to 'off-balance' parenting starting at the time of epilepsy onset and/or as reacting maladaptively to the changes in relation to the onset of epilepsy. Throughout follow-up, the group of children with epilepsy only performed less well than healthy classmates on measures of learning, memory span for words, attention and behaviour. After controlling for school delay, proactive interference (number of responses to the same images as in the learning trials, but now presented in reordered locations) was the only remaining variable that distinguished the group of children with epilepsy only. Group-wise, no changes in cognitive and behavioural differences over time were found, but instability in individual performances appeared to characterize children with epilepsy only. Rather than intrinsically epilepsy-related variables, such as idiopathic versus cryptogenic aetiology, seizure control or anti-epileptic drug treatment, the child's prediagnostic learning and behavioural histories and the parents' ability to continue their habitual parenting in the face of the diagnosis of epilepsy only were shown by both group-wise and case-by-case analyses to be important for understanding the cognitive and behavioural functioning of the children with epilepsy only.