We present a case of a 27-year-old male patient with Behcet's disease who presented with dyspnoea and haemoptysis in whom further investigation revealed a large and free right atrial thrombus and pulmonary thromboembolism. Considering the absence of haemodynamic compromise and the risk of recurrence after surgical treatment for cardiac thrombus, we preferred medical management which consisted of immunosuppression and anticoagulation. On a follow-up period of 12 months we observed complete dissolution of the thrombus and dramatic improvement of clinical status.