INTRODUCTION: Heparin-induced thrombocytopenia (HIT) is a relatively rare condition burdened by a high rate of complications and mortality. Cardiac surgery is a high risk setting for this condition. But in this area, some particularities can make both diagnosis and treatment difficult. Warfarin is often needed after valvular surgery but may be dangerous if HIT is ongoing. Danaparoid is the only anticoagulant whose mechanism of action has been demonstrated to counteract the pathogenesis of HIT. However, the 24-hour half-life challenges its use after surgery. CASE PRESENTATION: Here, we present a case in which HIT occurred six days after cardiac surgery. Warfarin was initiated two days after surgery but was stopped five days later, given the high risk of bleeding due to concomitant thrombocytopenia. HIT probability was initially underestimated, because a misleading diagnosis of endocarditis was made. When redo surgery was performed, no infectious masses were found, but a large thrombus was removed from the left atrium. Bivalirudin and danaparoid were used as alternative anticoagulants during the subsequent postoperative course. CONCLUSION: HIT should always be kept in mind after cardiac surgery, even if a more plausible cause of thrombocytopenia is present. Discontinuation of warfarin could lead to catastrophic consequences if an unrecognized HIT is ongoing, and an alternative anticoagulant is not started. Bivalirudin and danaparoid were used after the diagnosis of HIT, adapting anticoagulant therapy to the needs of recent surgery.