A 35-year-old morbidly obese woman with a history of deep vein thrombosis and pulmonary embolism presented for right atrial thrombectomy via AngioVac suction system. A portion of the thrombus could not be suctioned into the AngioVac cannula, leading to fragmentation and distal embolization with hemodynamic collapse. This sequence, observed in real time under transesophageal echocardiography, also demonstrated that the clot had echocardiographic features of chronicity. A well-organized chronic clot may be more difficult to extract via this method, leading to the complication described. With increasing popularity of this less invasive method, further investigation to understand the indications and contraindications is warranted.