Background. Thrombus formation is common after a Fontan operation. We investigated the frequency and location of thrombus in our population of children based on the type of Fontan operation performed.Methods and Results. Between January 1987 and January 1999, 592 patients underwent echocardiography after Fontan operation and 52 (8.8%) had intracardiac thrombus. Median age at Fontan operation was 1.9 years (range 0.8 to 35.1). Freedom from thrombus was 92%, 90%, 84% and 82% at 1, 3, 8, and 10 years after Fontan operation, respectively. There was no difference in freedom from thrombus, based on type of operation (atriopulmonary vs. lateral tunnel) or presence of fenestration. Thrombus was detected in the systemic venous atrium in 26 (48%), in the pulmonary venous atrium in 22 (44%), in both atria in 1 (2%), in the hypoplastic left ventricular cavity in 2 (8%), and in the ligated pulmonary artery stump in 1 (2%).Conclusions. Thrombus formation occurs with equal frequency in all types of modifications and is seen in the pulmonary, as well as the systemic venous atria. Our study suggests that thrombus formation is inherent to the physiology after Fontan operation and is not related to the type of modification performed.