We report the case of a patient with Behçet’s disease who presented with deep vein thrombosis and pulmonary embolism. In spite of being treated initially with anticoagulants, corticosteroid and oral cyclophosphamide, the patient presented again with a new pulmonary embolism. This critical situation made us initiate thrombolytic therapy with a urokinase ‘bolus’ followed by continuous infusion through a catheter into the pulmonary artery. Treatment response was good and 2 years later there was no evidence of new thrombotic episodes.