We have used immunohistochemical and histochemical techniques to identify patches of hepatocytes deficient in the enzyme cytochrome c oxidase, a component of the electron transport chain and encoded by mitochondrial DNA (mtDNA). These patches invariably abutted the portal tracts and expanded laterally as they spread toward the hepatic veins. Here we investigate, using mtDNA mutations as a marker of clonal expansion, the clonality of these patches. Negative hepatocytes were laser-capture microdissected and mutations iden- A dult tissue-specific stem cells are thought to reside within a specialized microenvironment, known as the niche, and it is here that stem cell behavior is regulated and maintained. 1 In epithelia with ordered structure and in a state of continual cell renewal, there is often a hierarchical organization with stem cells at the beginning of the flux, and terminally differentiated, reproductively sterile cells at the end of the flux, imminently to be lost from the population. Many studies have attempted to identify stem cells and the location of the niche using histological methods based on the premise that stem cells have inherent properties such as DNA label retention, high integrin expression, and abundant detoxifying enzyme activity. 2 However, many uncertainties remain even in comparatively well-defined instances such as the hematopoietic system. 3 It has been proposed that the gold standard of stem cell identification involves marking putative stem cells to identify the niche, and then performing lineage tracing to demonstrate that the proposed "stem cell" has multipotentiality. 4 This approach commonly uses mice genetically engineered to have a steroid-activated version of Crerecombinase knocked into the putative stem cell marker gene, such that Cre activation mediates excision of a roadblock sequence in the Rosa26-lacZ reporter, thus resulting in an irreversible marker in all the descendants of the putative stem cell. Using this technology, it has been shown, for example, that mouse hair follicle bulge cells expressing K15 generate all the epithelial cells in the lower hair follicle, 5,6 whereas in the murine small intestine, long-lived cell clones containing all the intestinal cell lineages can be generated from both leucine-rich repeat-containing G protein-coupled receptor 5 [Lgr5]-expressing 7 and polycomb ring finger oncogene [Bmi1]-expressing Abbreviations: 3D, mtDNA: mitochondrial DNA; PBS, SDH, succinate dehydrogenase. From the