Abstract Background Surgical excision of papillary breast lesions with atypia diagnosed using core needle biopsy (CNB) has been accepted; however, the management of benign papillary lesions (without atypia) has been controversial. The purpose of this study was to evaluate the surgical outcome of nonmalignant papillary lesions diagnosed by ultrasound-guided 14-gauge CNB, and to establish clear guidelines on management of these lesions. Methods We retrospectively identified 268 nonmalignant papillary breast lesions, including 203 benign lesions and 65 atypical lesions, diagnosed by CNB and subsequently surgically excised in 250 women at our institution between July 2004 and October 2010. For each lesion, medical records and radiologic and pathologic reports were reviewed and coded. We compared the histological upgrade among the collected variables. Results On histological examination after surgical excision, 15.4% atypical papillary lesions and 5.9% benign lesions were upgraded to malignant, and 20.2% benign lesions were upgraded to atypical. Atypia ( P  = 0.015) was significantly associated with malignant upgrade at excision. No clinical or radiologic variable was helpful in predicting the possibility of histological upgrade of CNB-diagnosed nonmalignant papillary lesions. Conclusions Nonmalignant papillary lesions diagnosed with CNB showed an unacceptable pathological upgrade rate after excision. Therefore, surgical excision should be performed for all papillary lesions of the breast for definitive diagnosis.