Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) has been recognized as a minimally-invasive and effective method for the diagnosis and nodal staging of lung cancer. We describe our initial experience with this method, including diagnostic sensitivity, safety, importance of obtaining histological samples, and diagnostic pitfalls. We retrospectively studied 100 patients (108 consecutive procedures) with radiologically suspicious intrathoracic lesions who were investigated by EBUS-TBNA. The procedures were performed between January 2005 and December 2011 at our institute. Adequate sampling value was 91.7%. Total diagnostic yield was 68.5% (74/108). In diagnosed subjects, malignancy and benign disease were identified in 68 and 6 cases, respectively. Diagnostic yield was relatively high in malignancy (88.3%), and poor in benign (19.4%). In the subgroup of malignant subjects, the diagnostic yield was higher in lung cancer (96.2%) than in other malignancies (72.0%) but, the difference disappeared if malignant lymphoma was excluded. No major complications were associated with the procedure. EBUS-TBNA is useful in accessing the circumference of the central airway tumor for diagnosis. Compared with previous studies, the diagnostic yield of mediastinal lymphoma and benign lesions is worse in our laboratory. Adequate tissue sampling and preparation are needed for the definitive diagnosis of malignant lymphoma and benign lesions.