Purified populations of functional stem cells are of great interest to the biomedical community, both in the understanding of stem cell biology and in clinical transplant settings. Studies continue to define phenotypic markers, functional characteristics and in vivo reconstitutional activity for both hematopoietic and non-hematopoietic stem cells. Historically, the capture of these pluripotent cells has presented a significant laboratory challenge. In transplant programs, for instance, peripheral blood stem cells from a stimulated donor usually represent 0.01% – 1% of the collected white blood cells and bone marrow contains 0.5% – 5% stem cells. A number of strategies have emerged for the purification of these cells, including high-throughput flow cytometry based on multiparametric immunophenotyping or immunophenotying in combination with functional characteristics. The MoFlo High-Performance Cell Sorter has proved invaluable in these efforts. In the experiment shown here, the MoFlo was used to purify bone marrow side population cells.