OBJECTIVE To evaluate the impact of coronary patterns with intramural arteries on the outcome of arterial switch operation (ASO) in neonates with transposition of the great arteries (TGA). METHODS Between 1987 and 2008, 919 neonates underwent ASO for TGA. Forty-six (5.0%) had intramural coronary arteries. Intramural course involved the left main coronary artery in 28 of the 46 cases (61%), the left anterior descending artery in 12 patients (26%), the right coronary artery in three and both right and left coronary arteries in three cases. Various techniques were used to manage the coronary arteries: ASO without coronary relocation in one, ASO with coronary transfer as a single coronary button in nine and ASO with coronary transfer as two separate buttons in 36 patients (additional pericardial patches were implanted to orientate the coronary button in nine cases or enlarge the coronary ostium in three cases). The intramural course was unroofed in most cases (after 1995). RESULTS There were 13 deaths (28%): two intra-operative, nine before discharge from the hospital and two after discharge; during the same period, overall mortality in the 873 neonates with other coronary patterns was 3.9%. Actuarial survival at 10 years was 71 + or - 7%. Most deaths (11/13, i.e., 85%) were related to coronary complications. No time-trend effect was noted regarding mortality. Non-fatal coronary lesions were detected in eight patients (three with clinical evidence of myocardial infarction and five without). Five patients underwent re-operation for coronary revascularisation. Actuarial freedom from coronary events at 10 years was 46 + or - 10%. After a mean follow-up of 8.3 + or - 4.8 years, left ventricular function was normal in 97% of the survivors; minor ischaemic sequelae were present in two patients. CONCLUSIONS Coronary patterns with intramural arteries remain associated with high coronary mortality and morbidity following neonatal ASO, even in the current era. The association of slit-like deformation of the ostium, stenosis of the intramural course and abnormal angle of take-off might explain the difficulty in coronary transfer. The technique of coronary transfer should be individually adapted to each anatomical situation. The place of patch ostioplasty of the intramural artery remains to be determined.