Objective To investigate the diagnosis and treatment of pulmonary arterial hypertension ( PAH) due to rare causes. Methods The clinical presentation, laboratory testing, diagnosis and treatment of 4 patients with PAH associated with rare causes in Beijing Anzhen Hospital from January 2001 to March 2008 were analysed retrospectively. Results Primary biliary cirrhosis, hyperthyroidism, antiphospholipid syndrome and pulmonary artery sarcoma may cause PAH, which were improved after corresponding diagnosis and management. Conclusion PAH can result from rare causes. The enhancement of its recognition will help earlier diagnosis and treatment and improve the prognosis.