With the growing number of cardiac pacemakers and internal cardioverter defibrillator implantations, problems with endocardial lead infection have been increasing. The newly developed Excimer Laser Sheath Lead Extraction System has been recognized as being highly useful for removing chronic infected leads. However, serious bleeding complications are a concern when this system is used. Here we report our experience with a 67-year-old man who was diagnosed with pacemaker endocarditis. Initially, lead removal was attempted using the Excimer Laser Sheath Extraction System, though this was abandoned because of severe adhesion of the leads and the junction of the supra vena cava (SVC) with the right atrium. Surgical removal of the leads was performed without using cardiopulmonary bypass and the leads were removed without any complications. During surgery, we found there was a silent perforation of the innominate vein brought about by the Excimer Laser Sheath System. Also, the junction of the SVC with the right atrium was thought to be an area potentially at high risk of perforation, because of a lack of surrounding tissue. It is our opinion that those who carry out procedures with the Excimer Laser Sheath System should understand the potential risk of perforation based on cardiac anatomy and should be prepared for lethal bleeding complications. Also, for emergent situations, we believe that close backup by a cardiovascular surgical team should be considered essential for performing the Excimer Laser Sheath Lead Extraction safely.