Patients with pulmonary embolism (PE) have a high risk of death and it is important to recognize factors associated with high mortality. N-Terminal pro-Brain Natriuretic Peptide (NT-pro BNP) has recently emerged as a promising biomarker for risk assessment in acute pulmonary embolism (PE). The aim of this study is to detect the in hospital prognostic value of NT-pro BNP in patients with acute (PE). Methods: This study included 64 patients diagnosed as (PE) with the mean age of 59.1 ± 16.5 years, 40 patients of them (62.5%) were male. All patients were subjected to 12 leads ECG. X-ray chest, laboratory tests including D-Dimer, troponin I, NT-pro BNP, Doppler ultrasound for the venous system of both lower limbs, Echocardiograhy and 64 multislices CT pulmonary angiography. Results: According to the admission level of NT-pro BNP our patients were divided into two groups: group I included 22 patients with normal NT-pro BNP (less than 300 pg/ml), and group II included 42 patients with elevated NT-pro BNP (more than or equal 300 pg/ml). Patients in group II were found to have a significantly higher incidence of heart failure (28.6% vs 4.6%, p = 0.025), impaired kidney function (serum creatinine was 1.7 ± 0.6 vs 1.1 ± 0.2, p = 0.018), tachypnea (85.7% vs 54.5%, p = 0.006) and cardiogenic shock (26.2% vs 0%, p = 0.014) but a significantly lower incidence of chest pain (21.4% vs 45.5%, p = 0.04) and lower left ventricular ejection fraction (51.3% ± 16.9% vs 67.3% ± 12.8%, p = 0.043) compared to group I. There were a significantly higher treatment with thrombolytic therapy (35.7% vs 9.1%, p =0.021) and positive inotropics (35.71% vs 4.55%, p = 0.006) in group II compared to group I. Also group II had a higher need for mechanical ventilation (26.12% vs 4.55%, p = 0.04) and a longer in hospital stay (19.5 ± 10.3 vs 5.3 ± 4.5, p = 0.001) than group I. The in hospital mortality was significantly higher in group II compared to group I (19.05% vs 0.0%, p = 0.042). Conclusion: Elevated NT-pro BNP levels in patients with (PE) are associated with worse short term prognosis in terms of higher morbidity and mortality and it could be used as a valuable prognostic parameter and good indicator for the need of more aggressive therapy.