Cardiac arrhythmias are well recognized sequelae of the Fontan operation for complex congenital anomalies. In this study the electrophysiologic effects of the Fontan procedure were evaluated in 30 patients who underwent cardiac catheterization with electrophysiologic study 1.9 +/- 1.3 years (mean +/- SD) after modified Fontan repair for functional single ventricle. Abnormalities of sinus node or ectopic pacemaker automaticity were detected in 50% (15 patients) by determination of a prolonged corrected sinus node or pacemaker recovery time. Total sinoatrial conduction time was prolonged in 50% of the patients with normal sinus rhythm. Sinus node or ectopic atrial pacemaker function was entirely normal in only 43% of patients. The predominant atrial rhythm was normal sinus in 70% and ectopic atrial or junctional in 30%. Abnormalities of atrial effective and functional refractory periods were noted in 43% of patients and were most pronounced at faster paced cycle lengths. Atrial endocardial catheter mapping revealed intraatrial conduction delays between adjacent sites in 76% of the patients tested and in eight of nine patients with inducible intraatrial reentry. Programmed atrial stimulation induced nonsustained supraventricular arrhythmias in 10% of the 30 patients and sustained arrhythmias in 27%. Intraatrial reentry was the most common inducible arrhythmia and was present in seven of the eight patients with sustained and two of the three patients with nonsustained atrial arrhythmias. Atrioventricular conduction abnormalities were noted in 10% (three patients). No patient had inducible ventricular arrhythmias with programmed ventricular stimulation. The electrophysiologic findings after Fontan repair include abnormal sinus node function, prolonged atrial refractoriness, delayed intraatrial conduction and inducible atrial arrhythmias.(ABSTRACT TRUNCATED AT 250 WORDS)