There have been several reports of a malpositioned pacemaker lead as a complication in pacemaker implantation. Herein we report a rare case of a malpositioned pacemaker lead in the left ventricle, which could occur in patients with cardiac structural abnormalities. A 70-year-old woman, who had undergone implantation of a pacemaker at the left subclavian position for complete atrioventricular block five years previously, was evaluated because of dyspnea and low grade fever. Echocardiography revealed a congenital atrial septal defect through which the lead was placed into the left ventricle. Whereas percuteneous lead removal seemed to be full of risk with concerns of thromboembolic events and infective endocarditis, the patient was referred to our hospital for surgical removal of the wire and closure of the defect. The lead was a screw-in type and removed and was extracted in the theatre using radiography. Intraoperatively it was found that the lead was positioned in the left ventricle apex after perforating the posterior mitral leaflet. Repair of the mitral valve perforation and closure of the septal defect and epicardial pacemaker lead implantation was performed. This case demonstrated the possibility of malposition of the pacemaker lead to the left ventricle in a transvenous pacemaker implantation procedure, which may lead to thromboembolic complication or infective endocarditis, and the pre-eminent role of echocardiography in the diagnosis of cardiac structural abnormalities. A malpositioned pacemaker lead in the left ventricle is a rare complication that can occur in patients with cardiac structural abnormalities. Lateral chest roentgenogram and echocardiography is efficient in preventing this complication. The removal of the lead in concerns of thromboembolic events and infection is preferable.