Infected cardiac thrombus is rare in children, with antibiotic or antifungal agents used as the first line of treatment. Persistence is an indication for surgical intervention. We describe two children who were treated successfully with a combination of antibiotic and antithrombotic agents. Use of antithrombotic agents promotes degeneration of fibrin, thus reducing the mass and facilitating the diffusion of the antibiotic and/or antifungal agents.