Despite the fact that thrombophilia is indisputable risk factor for venous thrombosis and pulmonary embolism (PE), its role in arterial thrombosis is not clear. Aim. To find out the role of thrombophilic states in the pathogenesis of deep vein thrombosis and effectiveness of pathogenetic prophylaxis of systemic thromboembolism. Material and methods. As a starting point we took the patients who underwent the first episode of venous thrombosis, thrombophilic state was diagnosed, then individual antithrombotic strategy was developed aimed at risk factors elimination and prevention of thrombotic events in each situation. The study included 84 patients. Patients were divided into two groups. 44 patients of the first main group were examined for thrombophilic states. If the diagnosis was confirmed, specific lifelong therapy was prescribed for correction of identified changes (if identified thrombophilia did not require long-term anticoagulation therapy (for example, hyperhomocysteinemia), anticoagulants were used in short course near 3 months after thrombosis according to current guidelines). The second control group consisted of 40 patients, in whom therapeutic dose of warfarin (INR 2—3) was selected with administration for 6 months followed by cancellation according to current standards. Results. There were significant differences between groups in the final result (arterial occlusion). Clear relationship of venous and arterial thrombosis and common pathogenic mechanisms were observed.