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Abstract Background A comprehensive evaluation of postoperative arrhythmias following surgery for congenital heart disease by continuous Holter monitoring has not been carried out. We aimed, firstly, to establish the time course of pre- and early postoperative arrhythmias by beat-to-beat analysis following cardiopulmonary bypass and, secondly, to examine which surgical procedures present risk factors for specific arrhythmias. Methods 494 consecutive patients, including 96 neonates, were studied with serial 24-hour Holter electrocardiograms before as well as uninterruptedly during the first 72 hours after surgery and prior to discharge. Results Within 24 hours of surgery 59% of the neonates and 79% of the older children developed arrhythmias. Junctional ectopic tachycardia occurred in 9% of neonates and 5% of non-neonates and ventricular tachycardia in 3% and 15%, respectively. For neonates, male sex and longer cross-clamping time independently increased the risk for arrhythmias (odds ratios 2.83 and 1.96/minute, respectively). Ventricular septal defect repair was a strong risk factor for junctional ectopic tachycardia in neonates and in older children (odds ratios 18.8 and 3.69, respectively). For infants and children, older age (odds ratio 1.01/month) and closure of atrial septal defects (odds ratio 2.68) predisposed to arrhythmias of any type. Conclusions We present the largest cohort of neonates, infants and children that has been prospectively studied for the occurrence of arrhythmias after cardiac surgery. Postoperative arrhythmias are a frequent and transient phenomenon after cardiopulmonary bypass, provoked both by mechanical irritation of the conduction system and by humoral factors.