The study of key mechanisms and molecules involved in the regulation of hematopoiesis in mouse models has been greatly facilitated by multi-parameter flow cytometry. Subpopulations of hematopoietic stem and progenitor cells can be identified and characterized using this technique. Furthermore, fluorescence-activated cell sorting (FACS) can prospectively isolate functionally-defined subpopulations of hematopoietic cells for use in further in vitro or in vivo analysis. The chapter describes methodology for preparing samples from mouse bone marrow, staining cells with fluorochrome conjugated antibodies, enrichment of HSC and progenitors, and finally data analysis.