Recently, a dispute has arisen concerning the operational definition and identification of epithelial stem cells. There is a current view which considers that epithelial stem cell identification depends solely on the in vitro isolation and expansion of cells from the putative stem cell. This article argues strongly that this is a perverse and erroneous view, and that lineage labelling, using genetic markers, remains the gold standard for identifying epithelial stem cells and for analysing their behaviour: in vitro methods show, at best, clonogenic potential but not fate, and constitute ancillary support for conclusions drawn from lineage analysis. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.