The role of thrombosis and hereditary thrombotic risk factors in the pathogenesis of chronic thromboembolic pulmonary hypertension (CTEPH) and non-CTEPH is not clear. We retrospectively analyzed the frequency of hereditary and acquired thrombotic risk factors in 245 patients with pulmonary hypertension, of whom 45 had CTEPH and 200 had non-CTEPH. Nine of 31 (29%) white patients with CTEPH versus 10 of 129 (7.8%) patients with non-CTEPH were heterozygous for factor V Leiden (FVL; P = 0.001). Contrary to other studies, antiphospholipid antibodies (APA) were not increased. Elevated factor VIII (FVIII) and von Willebrand factor (VWF; >1.5 U/ml) were common in CTEPH and non-CTEPH, although significantly higher (P = 0.01 for FVIII and 0.009 for VWF) in CTEPH versus non-CTEPH. There was no correlation between FVIII-VWF and fibrinogen levels in the CTEPH group (P = 0.84 for FVIII and 0.49 for VWF) but a strong correlation between FVIII-VWF and fibrinogen in the non-CTEPH (P < 0.0001). There was no association between FVIII-VWF and WHO functional status in the CTEPH group although there was a strong correlation (P < 0.001) between the two parameters in the non-CTEPH group. For equivalent WHO functional class, FVIII levels were significantly higher (P = 0.007) in the CTEPH group. We have found no association between FVIII-VWF levels and oxygen saturation in both groups of patients. The results indicate different pathophysiologies for CTEPH and non-CTEPH. The elevation of FVIII and increased incidence of FVL gene polymorphisms in the CTEPH group support a primary role of thrombosis in aetiology.