PURPOSE: To compare ultrasound-guided automated gun biopsy (USG-AGB) with ultrasound-guided fine needle aspiration (USG-FNA) in thyroid disease. MATERIALS AND METHODS: The findings of 156 patients who underwent both USG-AGB and USG-FNA were reviewed. The histopathologic results were categorized as group I (non-tumorous disease), group II (benign tumor), or group III (malignant tumor) on the basis of the results of USG-AGB and surgery. The results of USGAGB and USG-FNA were compared, and the agreement rate between the two was obtained. Based on the histopathologic results of USG-AGB, the sensitivity and specificity of USG-FNA were obtained for each histopathologic group. The histopathologic results obtained at surgery (n=38) and the findings of USG-AGB and USG-FNA were correlated. RESULTS: The pathologic agreement rate between the two methods was very high (kappa=0.805, p<0.01). Based on the histopathologic results of USG-AGB, the sensitivity and specificity of USG-FNA were, respectively, 100%/97.9% for group I, 94.7%/91.7% for group II, and 87.5%/97.1% for group III. When the results of USG-AGB and USG-FNA were correlated with the surgical results obtained in the 38 patients, 21.7 % (5/23) and 27.3 (6/22) of patients found at USG-AGB and USG-FNA, respectively, to be group II, were found at surgery to be group III, while in 93.3 % (14/15) and 81.3 % (13/16) of group II, the respective USG-AGB and USG-FNA findings, and those abtained at surgery, coincided. CONCLUSION: Although the agreement rate between USG-AGB and USG-FNA is high, USG-AGB is a potentially valuable tool in the diagnosis of thyroid malignant tumor, which can be missed at USG-FNA.