Morbidity and mortality of total cavopulmonary connection (modified Fontan procedure) may be decreased in many patients with single ventricle in whom the risk of surgery is high by performing the operations in a staged fashion. Each operative intervention, however, exposes the sinoatrial node region to risk of injury, and a multistaged approach may increase the risk of altered sinoatrial node function in these patients. The purpose of this study was to compare the prevalence of perioperative arrhythmias in patients undergoing either a primary or staged approach to the Fontan operation. Records were retrospectively reviewed for all patients having a Fontan procedure between January 1988 and December 1992. Of 324 patients undergoing a Fontan operation, 227 had a Fontan operation without a prior cavopulmonary shunt (group 1) and 97 had a cavopulmonary shunt before a Fontan operation (group 2). Arrhythmias were classified as altered sinoatrial node function, supraventricular tachycardia, or atrioventricular block. The prevalence of both transient (resolving before hospital discharge) and fixed (persisting until hospital discharge) altered sinoatrial node function was similar for the two groups after cavopulmonary shunt or primary Fontan despite a heterogeneous patient population (group 1: 10.6%/4.4%; group 2: 10.3%/3.1%; p = 0.28). Conversion from cavopulmonary shunt to Fontan in group 2 resulted in a higher prevalence of altered sinoatrial nude function in the early postoperative period (transient: 23.7%; fixed: 23.7%; p < 0.001) and on follow-up (group 1: 7.7%; group 2: 16.7%; p < 0.02). In group 2, 40 of 82 patients without arrhythmia after first intervention (cavopulmonary shunt) had an arrhythmia after the second intervention (Fortan) (49%); of 14 with an arrhythmia after the first operation, 10 (71%) had one at the second intervention (p < 0.01). In conclusion, a multistaged operative pathway to Fontan reconstruction is associated with a higher early risk of altered sinoatrial node function. The occurrence of altered sinoatrial node function after cavopulmonary shunt is itself a risk factor for arrhythmia after the Fontan operation. Longer follow-up is needed to assess the full impact of this finding.