Brain natriuretic peptide (BNP) has potent diuretic, natriuretic, and vascular smooth muscle-relaxing effects. BNP is elevated in heart failure and pulmonary disease with acute hypoxemia or cor pulmonale, and increases in proportion to the degree of right ventricular dysfunction. In this study we aimed to evaluate the time course of BNP levels in pulmonary embolism and to assess Its correlation with pulmonary artery pressure (PAP) and hypoxemia. Twenty-seven consecutive patients with acute pulmonary embolism (APE) and 26 healthy subjects were enrolled in this study. BNP levels were measured at admittance and at the end of the treatment. All patients’ arterial blood gas analyses were performed at admittance. Pulse oximetry testing was performed at the end of the treatment. Mean levels of BNP in patients with APE were significantly higher than those of the control group (358+350 vs 16±25 pg/ml, respectively, p<0.001) at admittance. In all patients, admittance BNP levels were significantly higher than discharge BNP levels (358±350 vs 32±25 pg/ml and 18±6 pg/ml, respectively, p<0.001 and p<0.05). Initial BNP levels significantly correlated with PAP (r=0.695, p<0.01). There was also a significant negative correlation between the BNP and P02 levels at admittance. We have shown that BNP levels decrease progressively during the course of APE, showing a positive correlation with PAP and a negative correlation with P02 and SpO2. This finding suggests that frequent BNP measurement can predict the course of APE and can be used to closely monitor the patients.