Abnormalities in cognition, academic performance and brain volumetrics have been reported in children with chronic epilepsy. The nature and degree to which these problems may be present at epilepsy onset or may instead become more evident over time remains to be determined. This study characterizes neuropsychological status, brain structure and their interrelationship in children with recent-onset epilepsy compared with healthy controls. Children (age: 8-18 years) with recent-onset idiopathic epilepsy (n = 53) and healthy controls (n = 50) underwent comprehensive neuropsychological assessment and quantitative volumetric measurement of segmented (grey and white matter) volumes of total cerebrum and lobar regions. Compared with controls, children with recent-onset epilepsy exhibit a pattern of mild diffuse cognitive impairment, regardless of epilepsy syndrome, as well as academic underachievement that in a subset of children antedates the first recognized seizure. There are no overall differences in MR morphometric analyses of total cerebral or lobar tissue volumes. Controls show a strong association between cognitive development and increasing cerebral tissue volume (especially white matter volume), an association that is absent in children with epilepsy. Children with a history of academic achievement problems exhibit the most abnormal cognitive function and have significant volumetric reductions in left occipital and parietal lobe grey matter. Patients with idiopathic epilepsy exhibit cognitive dysfunction and academic underachievement at the onset of the disorder, irrespective of epilepsy syndrome, and indications of antecedent neurocognitive impairment are present in a subset of children. Volumetric abnormalities are not yet apparent in the epilepsy group as a whole, but there are indications of an altered structure-function relationship in epilepsy, and the subset of children with prior history of academic problems have abnormal volume of posterior left hemisphere grey matter. These early abnormalities need to be integrated into lifespan models of the neuropsychology of epilepsy.