Columnar cell lesions are being increasingly identified in specimens excised for mammographically suspect microcalcifications. The entity of flat epithelial neoplasia remains a challenge for surgical pathologists due to its uncertain biological and clinical significance, inconsistent nomenclature, lack of prognostic data and the often unobtrusive and easily overlooked histological findings. This review aims to summarize our experience and the currently available literature on this topic, and will lead to a better understanding of this lesion. Because of its putative role as a precursor lesion and its many similarities to atypical ductal hyperplasia or ductal carcinoma in situ, differentiation from these lesions on the one hand and from columnar cell lesions without atypia on the other, is of importance and should result in different therapeutic recommendations depending on its presence in excisional or core needle biopsies.