Left atrial thrombosis in the absence of rheumatic heart disease and atrial fibrillation is a rare occurrence. We report two cases of left atrial pedunculated thrombus formation after orthotopic heart transplantation. Despite an uneventful post-operative course, sinus rhythm and normal contractility of the heart, large thrombi could be found several months following transplantation. Surgical thrombectomy was performed under cardiopulmonary bypass. Operative technique is proposed as one of the main factors that can contribute to left atrial thrombosis after heart transplantation.