Background: Exact mediastinal evaluation of patients with non-small-cell lung cancer (NSCLC) is mandatory to improve selection of resectable and curable patients for surgery. Mediastinoscopy (MS) and endoscopic ultrasound guided fine needle aspiration biopsy (EUS-FNA) are considered complementary, MS covering the anterior- and EUS-FNA the posterior mediastinum. Both methods can reach the paratracheal- and subcarinal-regions, but little is known about which method is most accurate, when compared in patients having both procedures performed. The aim of this study was to assess and compare the diagnostic value of MS and EUS-FNA with regard to mediastinal malignancy in the paratracheal- and subcarinal-regions. Methods: Sixty patients considered to be potential candidates for resection of verified or suspected NSCLC underwent MS and EUS-FNA. The EUS-FNA diagnoses were confirmed either by open thoracotomy, MS or clinical follow-up. Results: MS and EUS-FNA were conclusive for paratracheal or subcarinal mediastinal disease in 6 and 24 patients, respectively. Two patients with N2 disease diagnosed by EUS-FNA were upstaged to N3 by MS. The sensitivity for lymph node metastases in the right paratracheal region (2/4R) was 67% for EUS-FNA versus 33% for MS (p = 0.69). In the left paratracheal region (2/4L) the sensitivity of EUS-FNA was 80% versus 33% for MS (p = 0.06). In the subcarinal region (7) the sensitivity of EUS-FNA was 100% versus 7% for MS (p < 0.01). The sensitivity for lymph node metastases in region 2/4L and/or 2/4R and/or 7 was 96% for EUS-FNA versus 24% for MS (p < 0.01). Conclusion: In our hands EUS-FNA was superior to MS in the examination of paratracheal- and subcarinal-regions of patients considered for resection of lung cancer.