An association between macrovascular thrombosis and idiopathic inflammatory bowel disease has been described, although very few well-documented cases have been published. We report on a 39-year-old woman who presented with right hemifacial and upper limb edema that was shown to be due to an extensive right brachiocephalic vein thrombosis, diagnosed by magnetic resonance angiography. Laboratory findings suggested malabsorption, and a diagnosis of Crohn's disease was established. Moreover, elevation of the plasminogen activator inhibitor system was identified. This represents the first description of a spontaneous thrombosis in a patient with Crohn's disease involving the intrathoracic venous system and raises the possibility of impaired fibrinolysis being involved in the etiopathogenesis of this complication.