Objective: The purpose of this study was to evaluate the diagnostic accuracy and safety of performing transthoracic needle biopsy (TNB) under combined fluoroscopy and CT guidance using a C-arm cone-beam CT (CBCT) system. Methods: We evaluated the diagnostic accuracy and safety of performing TNB using a C-arm CBCT system. We retrospectively evaluated 99 TNB cases performed in 98 patients using a C-arm CBCT system with an 18-gauge automated cutting needle. We reviewed the diagnostic accuracy according to the size and depth of the lesion, incidence of complications, additional treatment for complications, procedure time, number of needle passes per biopsy and radiation dose. Results: The final diagnoses revealed 72 malignant and 27 benign lesions. The overall malignancy sensitivity, malignancy specificity and diagnostic accuracy were 95.8%, 100% and 97.0%, respectively, and those for small pulmonary nodules <20mm in size were 94.1%, 100% and 96.6%, respectively. There was no significant difference in the correct diagnosis of malignancy according to lesion size (p=0.634) or depth (p=0.542). For benign lesions, a specific diagnosis was obtained in 14 cases (51.9%). TNB induced complications in 19 out of 99 procedures (19.2%), including pneumothorax (16.2%), immediate haemoptysis (2.0%) and subcutaneous emphysema (1.0%). Among these, four patients with pneumothorax required chest tube insertion (2.0%) or pig-tail catheter drainage (2.0%). The mean procedure time, number of needle passes and radiation doses were 11.9±4.0 min, 1.2±0.5 times and 170.0±67.2 mGy, respectively. Conclusion: TNB using a C-arm CBCT system provides high diagnostic accuracy with a low complication rate and a short procedure time, particularly for small pulmonary nodules.