Heparin-induced thrombocytopenia (HIT) occurs in 1 to 3% of patients after cardiac surgery. In patients with suspected or confirmed HIT, the standard of care is withheld of heparin, and an alternative, non-heparin anticoagulant substituted. An established fact is that currently only direct thrombin inhibitors (lepirudin, bivalirudin and argatroban) and heparinoids like danaparoid are approved for alternative anticoagulation in HIT patients. Herein, we report the case of a patient who developed HIT after coronary artery bypass grafting (CABG) and who was successfully treated by the factor Xa inhibitor fondaparinux. Danaparoid is our first line alternative anticoagulant to treat HIT patients. Normally the recovery from thrombocytopenia began within 24 h. In the present patient, however, platelet counts continued to fall for 3 more days. Discontinuation of danaparoid and anticoagulation with fondaparinux clearly improved platelet counts which normalized. The present patient has been treated for 26 consecutive days, and we have not observed any subsequent fall in platelet counts and any further bleeding or thrombotic complications.