When any part of the pacemaker system is infected, all pacemaker hardware should be removed, because reinfection rates of 51% to 77% have been noted in patients whose infected pacemaker system has been only partially explanted. The removal of infected leads during cardiopulmonary bypass prevents mechanical injury as well as the spread of infection and vegetation. We report one case of endocarditis by staphylococcus aureus with infected transvenous pacing lead which was migrated into the heart from the left subclavian vein. We removed the migrated pacing lead and vegetation under cardiopulmonary bypass.