BACKGROUND Some studies have suggested that neurological development may be adversely affected in children with severe coronary heart disease who have undergone long periods of deep hypothermic cardiopulmonary bypass (CPB). Reports of cognitive function in VSD patients in whom surgical repair required only a relatively brief period of CPB are rare. Also, CPB is unnecessary for VSD patients undergoing transcatheter closure. The aim of this study was to assess the cognitive function in patients with ventricular septal defect. METHODS A total of 29 patients treated with surgery, and 35 treated with transcatheter closure and their age- and sex-matched best friends completed the cognitive P300 auditory-evoked potentials test and the intelligence test. RESULTS The patients and their best friends had normal intelligence quotient; however, the patients had longer P300 peak latencies in cranial frontal lobe and cranial vertex leads (329.2 ± 24.8 and 335.1 ± 20.0 ms) than the healthy controls did (319.1 ± 20.6 and 313 ± 18.2 ms) (P < 0.05). Patients who underwent surgery had longer P300 peak latency in the cranial frontal lobe and cranial vertex leads than did those with transcatheter closure and controls. When cardiopulmonary bypass and aortic clamping were used, the duration was associated with P300 peak latency for patients (P < 0.05). CONCLUSIONS VSD patients, especially those undergoing surgery, showed poor cognitive function, which may be associated with duration of cardiopulmonary bypass or aortic-clamping.