Biomarkers are needed for early risk stratification and improved inpatient management to obtain better outcomes in acute pulmonary embolism (PE) patients. The aim of the present study was to evaluate biomarkers of right ventricular dysfunction (RVD) in order to predict a complicated clinical course and long-term respiratory complications in acute PE.We retrospectively enrolled 50 consecutive patients hospitalized for acute PE. Plasma brain natriuretic peptide (BNP), troponin-I, fibrin degradation products, D-dimer, C-reactive protein, and arterial pH were measured to assess their prognostic significance. RVD was evaluated by echocardiography at admission, the clinical course during hospitalization was monitored for the development of complications (death, cardiopulmonary resuscitation, mechanical ventilation or circulatory shock), and the need for home oxygen therapy (HOT) was assessed at/after discharge.Thirty-two patients (64%) had RVD at admission, 6 (12%) developed a complicated clinical course, and 7 (14%) required HOT. Plasma BNP was significantly higher in patients with RVD (median value, 319.3 versus 50.5 pg/mL, P = 0.001). Plasma BNP was also significantly higher (median value, 1307.9 versus 102.6 pg/mL, P = 0.02) and arterial pH significantly lower (acidic) (median value, 7.371 versus 7.438, P = 0.008) in patients who developed a complicated clinical course. In addition, plasma BNP was also significantly higher in patients who required HOT (median value, 505.1 versus 91.1 pg/mL, P = 0.02). Plasma BNP at admission is not only a reliable marker of RVD and predictor of short-term prognosis, but also a predictor of long-term respiratory prognosis in acute PE patients.