Background: Early identification of patients with chronic thromboembolic pulmonary hypertension (CTEPH) may be critically important since it is associated with considerable morbidity and mortality. Recent studies suggest that CTEPH following acute pulmonary embolism may be more common than previously thought. The incidence of CTEPH after acute pulmonary embolism and associated risk factors are not well documented in China.Methods: A cohort study in a national referral institute was retro and prospectivelyconducted.Consecutive patients with acute pulmonary embolism admitted to the institute from January 1, 2006 toMarch 31, 2010 without previous confirmed pulmonary hypertension were included in our study. Duringfollow-up period, patients underwent echocardiography as screening test of pulmonary hypertension.Subsequently, if supportive findings were present, ventilation-perfusion lung scanning, right heartcatheterization and pulmonary angiography were used to confirm the diagnosis of CTEPH. According tocomprehensive assessment of medical history, clinical manifestations, results of echocardiography (asystolic pulmonary artery pressure greater than 50 mmHg), and other assistant examinations, CTEPH wasdiagnosed in patients who had not undergone right heart catheterization and pulmonary angiography.Results: From 2006 to 2010, 585 patients with acute pulmonary embolism were screened and 475patients were included in the study. Overall mortality after a median follow-up period of 24 months was18.5%. 215 patients were screened by echocardiography during the follow-up period. At the end of thestudy, seven patients were diagnosed with CTEPH, 2 of them underwent right heart catheterization andpulmonary angiography, and the other five patients were diagnosed through systematic evaluation by agroup of experts. The cumulative incidence of CTEPH after acute pulmonary embolism was 0.59% (95% Cl0.0~1.3%) at one year, 2.1% (95% Cl 0.3~3.9%) at two years, and 2.8% (95% CI 0.6~ 5.0%) at three years.No cases occurred after three years among the patients with more than three years of follow-up. A highsystolic pulmonary artery pressure at initial episode of acute pulmonary embolism (p=0.007, HR 1.040,95%Cl=1.011~1.070) and history of varicose vein of lower limb (p=0.048, HR 4.588, 95%C1=1.017~20.696)increased the risk of CTEPH.Conclusions: CTEPH is a relatively common, serious complication of pulmonary embolism. The cumulativeincidence of CTEPH after acute pulmonary embolism was at least 2.8% at three years. A higher pulmonaryartery pressure at the time of diagnosis of acute pulmonary embolism and history of varicose vein oflower limb may increase the risk of CTEPH.