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Background: Staging of lung cancer is essential to the treatment, which is curative only in cases of localized disease. Previous studies have suggested that endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is unnecessary when positron emission tomography-computed tomography (PET-CT) shows no mediastinal involvement. Objective: The aim of the study was to investigate how often EBUS-TBNA resulted in a clinically relevant upstaging in patients with lung cancer without mediastinal involvement at PET-CT. Methods: A total of 981 consecutive patients from 2009 to 2014 were referred for preoperative EBUS-TBNA. We included 167 patients with lung cancer without involvement of the mediastinum at PET-CT (115 N0 and 52 N1). Results: Of the 167 patients included, 10 (6.0%) were upstaged to N2 or N3 by EBUS-TBNA; 9 of these were originally classified as N1 at PET-CT. Therefore, 17.3% of the included N1 patients were upstaged to N2/N3 after EBUS-TBNA. This compares to only 0.9% of the N0 patients. After both EBUS-TBNA and PET-CT, 115 patients were operated, and 12 (10.4%) of these proved to be N2/N3. We calculated the sensitivity as 42.9%, the specificity as 99.0%, and the negative predictive value as 89.6%. Conclusions: The overall probability of a clinically relevant upstaging by EBUS-TBNA in patients judged as N0/N1 at PET-CT was 6.0%, compared to 0.9% in patients classified as N0 and 17.3% in patients classified as N1. The risk of overlooking N2/N3 disease after both PET-CT and EBUS-TBNA was 10.4%.