Endothelial progenitor cells (EPCs) and mesenchymal stem cells (MSCs) have emerged as potentially useful substrates for neovascularization and tissue repair and bioengineering. EPCs are a heterogeneous group of endothelial cell precursors originating in the hematopoietic compartment of the bone marrow. MSCs are a rare population of fibroblast-like cells derived from the bone marrow stroma, constituting approximately 0.001-0.01% of the nucleated cells in the marrow. Both cells types have been isolated from the bone marrow. In addition, EPC can be isolated from peripheral blood as well as the spleen, and MSC has also been isolated from peripheral adipose tissue. Several approaches have been used for the isolation of EPC and MSC, including density centrifugation and magnetic bead selection. Phenotypic characterization of both cell types is carried out using immunohistochemical detection and fluorescence-activated cell sorting analysis of cell-surface molecule expression. However, the lack of specific markers for each cell type renders their characterization difficult and ambiguous. In this chapter, we describe the methods that we use routinely for isolation, characterization, and genetic modification of EPC and MSC from human, rabbit, and mouse peripheral blood and bone marrow.