Deficiencies of natural anticoagulant proteins including antithrombin (AT), protein C (PC) and protein S (PS) are important risk factors for venous thromboembolism (VTE) in Japanese people. The identification of deficiencies of these proteins is important for the prevention and treatment of VTE. Genetic analysis can help in making a definitive diagnosis of these inherited deficiencies, and can be useful both for the individual and potential thrombotic risk to family members. Mutations of AT, PC and PS are usually detected by direct DNA sequencing and multiple ligation-dependent probe amplification (MLPA). Large cohort studies have shown that AT and PC mutations are identified in 85% and 70% of patients, respectively. On the other hand, the detection rate in PS deficiency is lower in around 40% of patients.