BACKGROUND: Pulmonary embolism (PE) is one of the most frequent diseases that could be missed in overcrowded emergency departments as in Turkey. Early and accurate diagnosis could decrease the mortality rate and this standard algorithm should be defined. This study is to find the accurate, fast, non-invasive, cost-effective, easy-to-access diagnostic tests, clinical scoring systems and the patients who should be tested for clinical diagnosis of PE in emergency department. METHODS: One hundred and forty patients admitted to the emergency department with the final diagnosis of PE regarding to anamnesis, physical examination and risk factors, were included in this prospective, cross-sectional study. The patients with a diagnosis of pulmonary embolism, acute coronary syndrome or infection and chronic obstructive pulmonary disease (COPD) were excluded from the study. The demographics, risk factors, radiological findings, vital signs, symptoms, physical-laboratory findings, diagnostic tests and clinical scoring systems of patients (Wells and Geneva) were noted. The diagnostic criteria for pulmonary emboli were: filling defect in the pulmonary artery lumen on spiral computed tomographic angiography and perfusion defect on perfusion scintigraphy. RESULTS: Totally, 90 (64%) of the patients had PE. Age, hypotension, having deep vein thrombosis were the risk factors, and oxygen saturation, shock index, BNP, troponin and fibrinogen levels as for the biochemical parameters were significantly different between the PE (+) and PE (–) groups (P<0.05).The Wells scoring system was more successful than the other scoring systems. CONCLUSION: Biochemical parameters, clinical findings, and scoring systems, when used altogether, can contribute to the diagnosis of PE.