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Tumours within the pulmonary arteries provide a diagnostic challenge due to their similar appearance to pulmonary emboli. Often, the decision to sample is multidisciplinary and the best approach to take is often unknown. Here we describe a case of urothelial carcinoma which metastasised to the mediastinum with evidence of tumour burden within the pulmonary artery. Sampling of this by endovascular and thoracoscopic means was unsuccessful; however, we were able to provide a diagnosis using direct visualization with endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). This report is the first of a central pulmonary artery tumour caused by urothelial carcinoma biopsied by EBUS-TBNA in the English literature. We describe the diagnostic challenges and steps in evaluating suspected tumour emboli with a focus on transbronchial needle aspiration.