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We present a case of a 54 years old female patient after anterior wall left ventricular myocardial infarction in 2005 who underwent coronary artery bypass graft (CABG) surgery requiring cannulation of the right internal jugular vein (IJV). She was admitted to a Department of Pulmonary Diseases with left bronchopneumonia (BPN) following 7 day treatment, with hemoptysis, dyspnoea and fevers. Duplex ultrasound (DUS) was used to diagnose flapping thrombus in the right IJV, severe thrombocytopenia and, in addition, progressing multiple infiltrates on X-ray a few days later. We empirically adjusted the treatment initiated in primary care and observed deterioration of the severe thrombocytopenia during treatment with low molecular weight heparine. We diagnosed heparin-induced thrombocytopenia (HIT) and, even though this indication was not included in our drug formulary, we initiated treatment with Arixtra (fondaparinux) 2.5 mg s.c. daily. Intensive conservative treatment was associated with significant clinical and laboratory improvement of the condition, significant regression of the IJV thrombus as well as the finding on X-ray. The final effective antibiotic treatment lasted 20 (amoxicillin + clavulanate) and 10 (clindamycin) days, respectively. Treatment with Arixtra (fondaparinux) continued in primary care and lasted a total of 65 days until normal thrombocyte levels were achieved, with gradual transition to oral anticoagulation treatment. The patient was discharged to primary care on the 23rd day of hospitalization when she was stabilized, a febrile and her cardiopulmonary functions were compensated. We did not identify any case of treatment of jugular thrombosis and concurrent HIT with fondaparin anywhere in the international literature.