Arrhythmia was compared between 40 consecutive patients (pts) undergoing atriopulmonary connection (APC) and 40 undergoing total cavopulmonary connection (TCPC), between 1986 and 1990. Patients were not randomized, and those undergoing APC predominantly had tricuspid atresia (57.5% versus 15%) compared with pts undergoing TCPC who had more varied and complex cardiac defects. Before surgery there was no significant arrhythmia in either group. Hospital mortality was 15/40 and 6/40 for APC and TCPC, respectively (p less than 0.05). Early after APC nine pts developed atrial flutter (AFL) and eight died, while after TCPC only two developed AFL, and neither died (p less than 0.01). Fatal junctional ectopic tachycardia occurred in one pt in each group. During follow-up (38 +/- 8.5 months after APC versus 20 +/- 10 months after TCPC), new arrhythmia was uncommon (two AFL after APC with one death versus two AFL and one supraventricular tachycardia after TCPC with no deaths). Ambulatory ECG during follow-up showed arrhythmia in two APC and six TCPC pts (p = NS). The incidence of early arrhythmia and mortality associated with early arrhythmia appears to be less after TCPC compared with APC.