The case of a patient affected with acute pulmonary embolism and concomitant cerebral thromboembolism is described. The patient was admitted to our Coronary Care Unit with aphasia and hemiplegia. Five days before, he had undergone a hip replacement. A lung scan showed bilateral embolism; transthoracic echocardiogram revealed signs of pulmonary hypertension and the presence of a large, elongated, highly mobile "in-transit" thrombus entrapped into a patent foramen ovalis, and prolapsing into the right and left ventricle during diastole. The patient underwent surgical removal of the thrombus, with closure of the patent foramen. We did not treat the patient with thrombolysis, fearing the damage that a new embolism might produce. After surgery, the patient had a lengthy hospital stay because of renal failure and infection due to Pseudomonas aeruginosa. The patient was discharged from the hospital three months later on dialytic treatment and although he was still aphasic, there was partial recovery of motor function. Nevertheless, normalization of renal function and regression of aphasia occurred during the following months, with a residual mild motor defect of the right hand. This case report represents a starting point for discussing treatment of "in-transit" thrombi during pulmonary embolism.