Use of central lines in the neonatal intensive care unit (NICU) has led to the formation of intracardiac thrombi. A paucity of data exists on the management of neonatal cardiac thrombi, with the few reported cases focusing on outcomes following thrombolytic therapy. This study was undertaken to evaluate the outcome of cardiac thrombi in neonates who do not receive thrombolytic therapy. Nineteen patients younger than 3 months of age diagnosed with cardiac thrombi were included. All 19 patients had a central line. Management consisted of a combination of antibiotics and low-molecular-weight heparin (n = 16) or surgical removal (n = 2). In one case, no treatment was instituted. One patient was lost to follow-up after partial resolution of the thrombus. Complete thrombus resolution occurred in 18 patients, 9 with negative blood cultures and 9 with positive blood cultures. It took longer for resolution of thrombi associated with positive blood cultures than for sterile thrombi. No patient had evidence of thrombus embolization. From these data we concluded that the natural history of cardiac thrombi is resolution. Infected thrombi require more prolonged therapy. Surgery is seldom required and thrombolytics are not usually necessary for clot resolution.