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This is a case report of a young 20-year-old male who was referred for an endobronchial ultrasound (EBUS) procedure to investigate a fever and a left hilar lymph node and patchy pleural-based opacities seen on CT of the chest. During the EBUS procedure besides the left hilar node, a large thrombus was noticed in the main pulmonary artery and another one in the right pulmonary artery. EBUS proved invaluable in making a diagnosis in an unsuspected case of pulmonary embolism.