Computer tomography-guided transthoracic needle aspiration (CT-TTNA) is a minimally invasive technique for sampling peripheral lung lesions. Radial endobronchial ultrasound-guided transbronchial biopsy (rEBUS-TBB) is an alternative. The present study analyzed and compared rEBUS-TBB and CT-TTNA in the diagnosis of peripheral pulmonary lesions (PPL).Clinical data of 513 patients with PPL who underwent an rEBUS-TBB or CT-TTNA examination were analyzed retrospectively. The positive diagnostic rate, complication rate, and influencing factors of the 2 methods were compared.The positive diagnostic rate and complication rate were significantly higher in CT-TTNA than rEBUS-TBB (P = .001; P < .001, respectively). The rEBUS-TBB group showed a higher positive diagnostic rate in larger lesions (>2 cm) than in smaller (≤2 cm) (P = .012), and was lower in the lesions proximal to the chest wall than those distally located (P = .046); no significant difference was observed in the different pulmonary segments (P = .109). In the CT-TTNA group, the positive diagnostic rate in larger lesions did not differ significantly than the smaller lesions (P = .05); it differed significantly in different segments (P = .044). The incidence of pneumothorax was lower in lesions proximal to the chest wall than those located distally (P = .037). In the rEBUS-TBB group, the success rate of the exploration and biopsy of the lesions was 87.4%; the rate of exploration of larger lesions and with bronchial sign was higher than smaller lesions and without bronchial sign (P < .001; P < .001, respectively) while that of lesions close to the chest wall was lower than those distally located (P = .006).rEBUS-TBB and CT-TTNA are effective and safe in the diagnosis of PPL. The positive diagnostic rate of CT-TTNA is higher than rEBUS-TBB. The incidence of pneumothorax in CT-TTNA is higher than rEBUS-TBB. CT-TTNA is selected for smaller lesions close to the chest wall; rEBUS-TBB is used for lesions larger, distal from the chest wall or with a bronchial sign.