We describe a 34-year-old female patient with recurrent thromboembolic events, most recently with occlusion of the superior mesenteric vein - despite regular intake of oral anticoagulation with Apixaban at the dosage recommended by the manufacturer. The underlying cause was enteral malabsorption with protein loss syndrome due to active Crohn's disease, limited to the small intestine, with an atypical clinical presentation. We discuss the topic of anticoagulation in the presence of an enteral barrier disorder.