Our report suggests that high mitochondrial mass, quantified using live MitoTracker staining, is associated with a number of stem cell characteristics and biological functions including CSC markers ALDH+, ESA/CD24, large cell size, mammosphere formation in vitro, as well as tumor-initiating activity in vivo. Moreover, cells with high mitochondrial mass were preferentially resistant to paclitaxel during mammosphere formation and the comet assay (a marker DNA damage), when compared to low mitochondrial mass cells. Thus, we conclude that high mitochondrial mass can be used as a biomarker to isolate a sub-population of stem-like cancer cells that are chemo-resistant. This has important implications for better appreciating the role of tumor metabolic heterogeneity in driving chemo-resistance and treatment failure, via recurrence and metastasis.