We present two patients investigated using computed tomography (CT) and found to have a thrombus lodged within a patent foramen ovale (PFO) in association with pulmonary embolism. One patient was managed with emergency surgical embolectomy because of the risk of fragmentation and systemic embolization, and the other was managed conservatively because of significant pulmonary hypertension and inferred high surgical risk. Free-floating thrombus straddling a PFO has been previously reported using transoesophageal echocardiography (TOE); however, the CT appearance of this entity has not been previously documented. The detection of thrombus trapped within a PFO is an important finding with significant management implications for the patient. These cases highlight the importance of reviewing the interatrial septum on CT examinations of the thorax.