Purpose: To compare the efficacy and safety of CT-guided automated gun biopsy with those of fine needle aspiration biopsy of pulmonary lesions. Materials and methods: Under CT guidance, we performed automated gun biopsies in 115 cases of 109 patients and fine needle aspiration biopsies in 119 cases of 108 patients with pulmonary lesions. Between the two methods, we compared the diagnostic rate, diagnostic accuracy and frequency of complications according to the depth and diameter of pulmonary lesions. Results: The overall diagnostic rates of automated gun biopsy and fine needle aspiration biopsy were 76.5%(88/115) and 64.7%(77/119) respectively. There was a significant statistical difference (p=0.048), especially in the case of malignant lesions less than 3 cm(p=0.027) and more than 6cm (p=0.008) in maximal diameter. The diagnostic accuracy of automated gun biopsy and fine needle aspiration biopsy showed significant statistical difference only in malignant lesions more than 6cm in maximal diameter(p=0.008), and in the lesions located from 1cm to less than 3cm from the pleura(p=0.030), as seen on CT. There was no significant statistical difference in the frequency of complications. Conclusion:Automated gun biopsy of pulmonary lesions under CT guidance is safe, with complications rate comparable to those of fine needle aspiration biopsy. A higher overall diagnostic rate can be achieved by automated gun biopsy than by fine needle aspiration biopsy. For the diagnosis of pulmonary lesions under CT guidance, automated gun biopsy is therefore a more useful procedure than fine needle aspiration biopsy.