We studied the value of routine neonatal electrocardiography (ECG) in the 1st 48 hours of life to diagnose congenital heart disease in 37 neonates with Down syndrome. Twenty-four infants had no clinical evidence of congenital heart disease, had normal ECGs and normal cardiac anatomy on echocardiography. Thirteen children (35.2%) had congenital heart disease. The ECG was normal in seven infants with congenital heart disease: four with atrial septal defect (ASD), two with tetralogy of Fallot (TOF) and one with ventricular septal defect (VSD). A left QRS axis deviation was found in six infants: five with complete atrioventricular septal defect (AVSD) and one with VSD and mitral valve prolapse. However, only the five infants with complete AVSD had a superior QRS axis. Although neonatal ECG detected the presence of complete AVSD in neonates with Down syndrome, it missed an equal number with other heart defects. Echocardiography remains the way reliably to diagnose or exclude congenital heart disease in these infants.