Few data are available on the clinical course of Japanese patients deficient in natural anticoagulants (antithrombin (AT), protein C, and protein S). We conducted a nationwide survey to reveal the clinical course of these patients. Questionnaires were sent to 321 council members of the Japanese Society on Thrombosis and Hemostasis, Japanese Society for Vascular Surgery, and Japanese Society of Phlebology. A total of 103 responses were obtained and data of 183 patients were collected. Of 183 patients, 142 (78%) experienced at least one episode of venous thromboembolism (VTE). The first VTE occurred before the age of 40 years in 71 patients (45%). Venous thromboembolism recurred in 15 (39%) patients with AT deficiency and 19 (18%) patients with other deficiencies. These findings suggest that half of the first episodes of VTE in patients deficient in natural anticoagulants occur before middle age and the risk of VTE recurrence is high in patients with AT deficiency.