Nephrotic syndrome represents a form of acquired thrombophilia thereby causing increased risk of thrombosis. In patients with nephrotic syndrome both venous and arterial thrombosis can occur; however, intracardiac thrombus is among the rarest reported in the literature. In this case report, we present a 10.5-yr-old boy with right atrial thrombosis and an acute rejection episode after renal transplantation due to end stage renal disease caused by focal segmental glomerulosclerosis manifested by nephrotic syndrome. The clinical course was successfully managed with surgical removal of thrombus, institution of anticoagulant as well as antirejection therapy. This report draws attention to the risks that could be associated with thrombosis in renal recipients with congenital or acquired thrombophilias and emphasizes the importance of identifying risk factors for thrombosis in these patients.