The aim of this study was to determine the role of vacuum-assisted biopsy (VAB) in patients with ultrasound imaging-histologic discordance during 16-gauge core needle biopsy (CNB) and to compare VAB with vacuum-assisted removal (VAR) in diagnostic accuracy in patients with ultrasound imaging-histologic discordance. From January 2006 to October 2008, a consecutive biopsy was performed on 1532 lesions with ultrasound-guided 16-gauge CNB. Sixty two lesions were considered to be ultrasound imaging-histologic discordant. Among the 62 lesions, 55 lesions underwent subsequent VAB or VAR, which made up our study population. Among the 55 cases, 22 underwent subsequent US-guided VAR, and the other 33 lesions underwent subsequent US-guided VAB. All malignant lesions at VAB and VAR got subsequent surgery, and all benign lesions at VAR or VAB were followed up for at least 1 year. Five lesions of the VAR group were diagnosed as having carcinoma (5/22, 22.7% of pathologic changing rate). Seven lesions of the VAB group were diagnosed as having carcinoma (7/33, 21.2% of pathologic changing rate). Subsequent surgery further demonstrated the diagnosis of VAB for all the lesions with pathologic change. There was no significant difference in pathologic changing rate between these two groups (p < 0.05). A US-guided VAB was a valuable alternative to VAR or surgery excision to obtain definitive diagnosis in patients with breast lesions showing imaging-histologic discordance during 16-gauge CNB.