A 39 year old man with normal, stable blood pressure was admitted to the Cardio-Pulmonary Intensive Care Unit due to diagnosed spiral CT pulmonary embolism (PE) and deep venous thrombosis (DVT). In 1999, a hereditary antithrombin (AT) deficiency was confirmed in the presented case. In 2006, because of a knee injury, the patient was provided with a plaster cast and primary antithrombotic prophylaxis with low molecular weight heparin (LMWH) (80 mg of enoxaparin) was administered subcutaneously once a day (patient's weight was 80 kg). Despite prophylaxis PE and DVT occurred after 6 weeks of treatment. The patient was successfully treated with unfractioned heparin, repeated infusions of AT concentrate and oral anticoagulants (OA). Transient pulmonary hypertension documented by echocardiography and hemoptysis complicated course of PE. Secondary prophylaxis with OA, and INR maintenance between 2-3, was successfully continued.