Background and objectives. Brain-natriuretic peptide (BNP) is a potent natriuretic, diuretic hormone that is released from heart into the circulation. We aimed to investigate whether N-terminal-pro-BNP (pro-BNP) could predict localisation of thrombus in patients with acute pulmonary embolism. Methods. Emergency patients found to have thrombosis in the pulmonary artery on helical computed tomography were enrolled. The thrombi which were localised in the main/right or left pulmonary artery were classified as central and those at segmentary/sub-segmentary levels as peripheral. The patients were evaluated by an echocardiogram and pro-BNP levels were measured. Results. Forty-nine patients were enrolled. The thrombus was unilateraly located in 63.3 percent patients and peripherally in 81.6 percent. The difference in pro-BNP levels between those with central and peripheral thrombi was significant (p<0.05). Pro-BNP levels of patients with and without evidence of right ventricular overload (pulmonary hypertension, right heart dilatation, interventricular septal hypokinaesia) were also significantly different (respectively, p<0.001, p<0.01, p<0.01). The pro-BNP levels of patients who were followed up in the intensive care unit and needed thrombolytic treatment were significantly higher (respectively p<0.001, p<0.01). Conclusions. Higher pro-BNP levels indicate higher probability of more central location of thrombus, resulting in a more adverse clinical course. Further studies are needed to determine the predictive values of pro-BNP levels for localisation of pulomnary embolus.