This study compares the acute cognitive effects of short nonconvulsive seizures with the effects of interictal epileptiform electroencephalographic (EEG) discharges in children. The study is a prospective, standardized, nonrandomized, and open clinical comparative study. Eligible patients were included when they had (a) unclear seizures and fluctuations in cognitive performance and (b) frequent epileptiform EEG discharges in a recent EEG. All children were assessed with EEG/video (Brainlab) simultaneously with computerized neuropsychologic testing (FePsy) assessing motor speed/alertness, mental speed/attention, and memory function. Eleven patients with short nonconvulsive seizures during cognitive testing were included and compared with 11 matched patients with interictal epileptiform EEG discharges during cognitive testing but without seizures. Patients included in both groups had a reconfirmed diagnosis of epilepsy. Cognitive performance for both groups was compared. Statistical analysis showed significant correlations between the number of seizures (during cognitive testing) and impaired alertness and between the duration of the ictal period and memory impairment. Interictal epileptiform EEG discharges do not have an additional independent effect on cognitive function. The results demonstrate the accumulating cognitive effect of seizures and illustrate that frequent seizures, even when these are short in duration and with subtle symptomatology, can have a substantial impact on daily life and can lead to state-dependent learning impairment. Alertness and short-term memory appeared to be the functions that are most vulnerable for the acute effects of seizures.