In transposition of the great arteries, systemic venous return is preferentially routed to the aorta, and any spontaneous or iatrogenic emboli may therefore cause organ infarction. We present a patient with transposition of the great arteries who developed myocardial infarction prior to balloon septostomy and, also, was later documented to have sustained brain infarction despite adequate precautionary measures. Minimal handling of venous sites in these patients is crucial.