We present the successful treatment of a large solid right atrial thrombus by the catheter-based suction embolectomy system AngioVac® (AngioDynamics, NY, USA). A previously healthy 60-year-old male was referred with acute pulmonary embolism, a large deep vein thrombus and a large right atrial thrombus. After one week of anticoagulation, the size of the atrial thrombus was unaltered, and the patient was treated by catheter-directed embolectomy using the AngioVac system. The solid thrombus occluded the catheter during the procedure. With the vacuum maintained, the occluded catheter was removed from the patient and the thrombus mass was removed. The remaining atrial thrombus was successfully removed by suction after the reinsertion of the catheter. The patient recovered well and was discharged 7 days after the procedure. The therapy was safe and minimally invasive.