Junctional ectopic tachycardia after surgical repair of congenital heart defects is associated with high mortality. Usually, it is transitory and resolves spontaneously, but a long period with very fast heart rate and without atrio-ventricular synchrony contraction may cause low cardiac output. Treatment with common anti-arrhythmic drugs is often uneffective both in restoring sinus rhythm and in reducing heart rate. Since hypothermia is known to decrease cardiac automaticity, two infants, aged 4 and 10 months, with junctional ectopic tachycardia and low cardiac output after surgical repair of the atrio-ventricular septal defect were treated with hypothermia after unsuccessful pharmacological attempts to control the arrhythmia. Generalized hypothermia was induced with cooling-blankets and ice packs. Rectal temperature initially dropped to 30 degrees and was subsequently maintained at between 33.8 and 34.2 degrees with the heart rate between 130 and 140 m beats per minute. Trans-oesophageal atrial pacing at a higher rate allowed for sequential atrio-ventricular contraction. Signs of low cardiac output were quickly resolved. One patient was warmed-up after 12 hours of hypothermia and remained in sinus rhythm. In the other patient, the arrhythmia recurred after rewarming and a further 30-hour period of hypothermia was required. Sinus rhythm was maintained thereafter. Both patients are in stable sinus rhythm 20 and 22 months after surgery. Our experience supports the use of hypothermia as a means to control post-operative junctional ectopic tachycardia resistant conventional anti-arrhythmic drugs.