Columnar cell lesions of the breast refer to the morphological spectrum of alterations of the epithelial lining of variably dilated acini of the terminal duct lobular unit (TDLU), often related to secretions and calcifications. After decades of varied terminologies, the term of 'flat epithelial atypia' by the World Health Organization (WHO) consensus group encompasses the part of the spectrum where columnar cell change or columnar cell hyperplasia acquires low grade cytological atypia, merging with atypical ductal hyperplasia and low grade ductal carcinoma in situ. Its association with low grade invasive carcinoma and lobular neoplasia, whether by proximity to these lesions, or by similar molecular expressions, has prompted greater scrutiny into its clinical significance. Although recent literature attempts to refine the term 'flat epithelial atypia', the applicability of its morphological criteria in routine diagnostic practice remains to be seen, and interobserver variability is highly possible. This poses even greater challenges especially in limited samples of breast tissue, such as in core biopsies, for pre-operative decision-making. The purpose of this review is to elucidate evolving clinical and diagnostically relevant principles that surround and influence the significance of this still controversial entity, especially when discovered on core biopsy in the initial phase of breast diagnosis and management.