In patients with respiratory failure and impairment of the left ventricle, arteriovenous extracorporeal membrane oxygenation (ECMO) offers further therapeutic options. Systemic anticoagulation is mandatory and heparin is routinely administrated. However, repeated exposure to heparin may cause heparin-induced thrombocytopenia (HIT) and carries a risk of thrombotic mortality and morbidity. We present a patient who developed HIT during ECMO support and was treated successfully and safely by fondaparinux. Fondaparinux can be used for thromboembolic treatment or prophylaxis in a patient with HIT.