The tumor-initiating cells, or cancer stem cells (CSC), has been hypothesized to represent the chemo-resistant and disease-propagating fraction in leukemia and various types of solid tumors.Therefore targeted therapy against CSC may represent a novel therapeutic strategy to eradicate cancer more effectively and reduce the risk of relapse.Developing such targeted therapy requires molecular characterization of the similarities and differences between normal adult stem cells and cancer stem cells; yet such a task has proven challenging due to the relatively low frequency of these cell types.We have developed a multi-plexed TaqMan(R)-based miRNA detection strategy that allow rapid and accurate miRNA profiling from small number of cells or even at single cell level.Applying this strategy, we have systematically analyzed the miRNA expression profile of FACS-purified AML leukemia stem cells (LSC), leukemia blasts as well as normal human bone-marrow derived hematopoietic stem cells and committed progenitors.Distinct miRNA signatures were identified characterizing each of these cell populations.Unique miRNA profiles were also determined for cancer stem cells derived from solid tumors, such as bladder cancer.Characterization of these candidate miRNAs revealed potential pivotal regulatory roles of miRNAs in cancer stem cell function, cancer pathogenesis and metastasis.