Breast cancer is known to show considerable inter-tumoural heterogeneity. It is widely accepted that combinations of oncogenic events have a major role in determining tumour phenotype. However, accumulating evidence suggests that the identity of the cell that acquires the first oncogenic event, the so-called cell of origin, may define the molecular subtype of the resulting tumour. Recent work published in the Journal of Pathology by Natrajan and colleagues questions the origin of breast cancer heterogeneity. After studying BRCA1 tumours, they suggest that genomic alterations are not sufficient to determine tumour behaviour. These and other recent observations underscore the importance of defining what is causing tumour heterogeneity, so that appropriate therapy can be given.