Background: Mediastinal lymphadenopathy in patients with malignancy is a common clinical problem in tuberculosis-endemic countries. The recently developed endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) procedure enables direct and real-time aspiration of mediastinal and hilar lymph nodes. The aim of the study was to determine the efficacy of EBUS-TBNA results in the evaluation of mediastinal lymph nodes in patients with extrathoracic malignancy. Materials and Methods: Retrospective analysis was performed in 40 patients with proven (n = 38) or suspected metastasis of unknown origin (n = 2) who underwent EBUS-TBNA between July 2007 and August 2011. Results: All 40 patients successfully underwent EBUS-TBNA and no complications were observed. EBUS-TBNA diagnosed metastasis from extrathoracic malignancy in 16 (40%) patients, new lung cancer in 2 (5%), reactive lymph node in 9 (22.5%), sarcoidosis in 5 (12.5%), anthracosis in 5 (12.5%) and tuberculosis in 3 (7.5%). The diagnostic sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy of EBUS-TBNA based on the number of patients were 90.0%, 100%, 100%, 90.9% and 95.0%, respectively. In 33 patients with available data of fluorodeoxyglucose positron emission tomography (PET)/computed tomography (CT) scans, the diagnostic sensitivity, specificity, PPV, NPV and accuracy of PET/CT scan based on the number of patients were 94.7%, 35.7%, 66.6%, 83.3%, and 69.6%, respectively. The association between larger lymph node size on EBUS and malignancy of lymph node sample on pathological examination was statistically significant (P = 0.018). Conclusions: EBUS-TBNA is a sensitive, specific, minimally invasive and a safe procedure for the diagnosis of mediastinal and hilar metastasis from extrapulmonary malignancy in a tuberculosis-endemic country.