The development of a convex probe endobronchial ultrasound (CP-EBUS) videobronchoscope to allow real-time transbronchial needle aspiration (TBNA) has been a significant advance in minimally invasive lung cancer staging and diagnosis. Several recent studies have demonstrated CP-EBUS-TBNA to have recovery rivalling that of the current gold standard, cervical mediastinoscopy. These same studies have indicated that the safety of this procedure has no reported complications.The present case study presents two infectious complications from full extension endobronchial ultrasound transbronchial needle aspiration and discusses possible aetiologies of these infections, as well as implications for future application of this technology.