To compare the diagnostic yields and complication rates of transthoracic fine needle aspiration cytology(FNAC) and gun biopsy in the diagnosis of pulmonary mass, a retrospective review was performed in 125 cases. Under the fluoroscopic guide, FNAC was performed by 20G Chiba needle in 91 cases, core biopsy was done by 18.5 G vaccum needle attached with automated biopsy gun in 74 cases and both procedures were done together in 37 cases. Overall sensitivity was 88.4% in FNAC and 87.5% in gun biopsy. For malignant pulmonary tumors, correct type correlation with final diagnosis was obtained in 33(76.7%) out of 43 cases by FNAC and 30(75.0%) out of 40 cases by gun biopsy. For benign pulmonary lesions, there were correct type correlation in 14(35.0%) out of 40 cases by FNAC and 14(53.8%) out of 26 cases by gun biopsy. The complication was pneumothorax and hemoptysis. Pneumothorax occured in 11.1% of FNAC, 10.9% of gun biopsy and 10.9% of both technique, among which chest tube drainages were necessary in one patient by gun biopsy and in three patients by both technique. Although no significant difference of diagnositc accuracy and complication rate was found between FNAC and gun biopsy, gun biopsy was more helpful in the diagnosis of pulmonary benign lesions than FNAC.