Image-guided biopsies of the breast play an integral role in the diagnostic evaluation of mammographically detected calcifications. Apart from cancer, on these biopsies we are increasingly recognising a hitherto poorly categorised group of benign to atypical entities collectively known as columnar cell lesions. A variant of this theme is flat epithelial atypia, a columnar lesion characterised by mildly atypical epithelial cells. There is emerging evidence to suggest that flat epithelial atypia may represent a precursor of or the earliest morphologically recognisable form of low-grade ductal carcinoma in situ. In addition, these lesions are often associated with tubular carcinomas and lobular neoplasia. This article reviews the current concepts and controversies surrounding flat epithelial atypia, with special emphasis on the biology, histological and clinical features. Potential diagnostic challenges faced by pathologists in the evaluation of these atypical columnar lesions are also discussed.