This report describes a rare case of complete transposition of the great arteries (TGA) with an intramural right coronary artery arising well above the sinotubular junction. Additionally in this case, the left circumflex artery arose anomalously as a branch from the right coronary. Identification of this anatomic anomaly was made by transthoracic echocardiography before surgery. The patient underwent a successful arterial switch operation on day 6 of life. Due to the preoperative diagnosis of the unusual right intramural coronary artery, the coronary transfer technique during the arterial switch was altered, allowing preservation of the right coronary artery.