Tissue clonality can be assessed in females by analyzing the methylation status of polymorphic DNA markers on X-linked genes because extensive de novo methylation of one allele at the preimplantation stage is associated with its permanent inactivation. We applied X chromosome inactivation toward understanding human breast morphogenesis by examining the nonmalignant breast epithelium from two reduction mammaplasties and a mastectomy. We found that entire lobules and large ducts of normal breast tissue have the same X chromosome inactivated, suggesting that they are derived from the same stem cell. The regions of inactivation of a particular X chromosome do not extend over an entire breast, so that ducts and lobules with opposite chromosomes inactivated are present within a single breast. Potential relevance of these observations for malignant transformation is discussed.