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A case of a two month infant with complex congenital heart disease (aortic coarctation with ventricular septal defect) associated to a cellular brain migration failure is presented. The management strategy consisted on the correction of congenital heart disease by means of a two-stage surgery without a further preoperative evaluation of the neurological status. The patient developed several perioperative complications such as two episodes of cardiac arrest, reconnection to cardiopulmonary bypass, cardiac tamponade, chilothorax and septic shock. A neurological protocol consisting in electroencephalography, brain magnetic resonance and Single Photon Emission Computed Tomography (SPECT) was practiced during the postoperative period, which detected microgyria with paquigyria and a cellular brain migration failure was suspected. The final outcome was death due to multisystemic failure and the autopsy confirmed the neurological disease, as well as poor life function prognosis. Should the heart-brain binomial had been considered in an integral preoperative evaluation, the therapeutical approach could have been modified.