The distinction between benign and malignant papilloma of the breast through percutaneous needle biopsy can be difficult because of limited samples; the underestimation rate can be up to 25%. The aim of this study is to identify clinical and histological factors associated with underestimation, invasive ductal carcinoma, or ductal in-situ carcinoma (DCIS) of the breast found in surgical specimens from papillary lesions. This may contribute toward selection of patients for a follow-up strategy without the need for surgical excision. From a database of 3563 patients, we identified 85 with intraductal papilloma between 2007 and 2013 who had undergone breast-imaging studies, percutaneous needle biopsy, and surgical resection of the lesion. Central papillomas normally present with a palpable mass, whereas peripheral papillomas generally do not have clinical manifestations (microcalcifications); both central and peripheral papillomas were related to atypical lesions, 13.5 and 15.4%, respectively. Among the 59 cases of central papillomas, there were four cases of underestimation, three DCIS and one invasive ductal carcinoma (6.8%). Among the 26 cases of peripheral papillomas, there was one case of DCIS (3.8%), with a total underestimation rate of 5.8%; all underestimated lesions measured more than 1 cm. The median size was 11 mm at mammography and 19 mm at ultrasound. Our data suggest that lesions less than 1 cm in size, without atypia and concordant imaging and clinical findings, may not require surgical resection.