The substrate of paradoxic embolization is a patent foramen ovale allowing right-to-left passage of embolic material. A thrombus in transit entrapped by a patent foramen straddling an atrial septal aneurysm is an exceedingly transient condition rarely documented on imaging studies. We present the case of a 67-year-old man with acute pulmonary embolism and concomitant cerebral infarction found to have a large thrombus traversing a patent foramen ovale. Intraoperative real-time three-dimensional transesophageal echocardiography allowed accurate spatial characterization of the thrombus and correlated closely with surgical findings. It provided more realistic intraoperative guidance compared with conventional two-dimensional transesophageal echocardiography.