It has long been recognized that single therapies, such as G-CSF, have a limited capacity to mobilize hematopoietic progenitor cells from the bone marrow. As a consequence in ∼20% of patients insufficient numbers of HPCs are mobilized to perform a bone marrow transplant. Recent studies have shown synergistic mobilization of HPCs when G-CSF pretreatment is combined with acute administration of a CXCR4 antagonist suggesting that combinatorial therapies may have therapeutic potential. In addition to HPCs, endothelial progenitor cells (EPCs) and mesenchymal stem cells (MSCs) reside in the bone marrow. These progenitor cells contribute to tissue regeneration and there is currently much interest in identifying the factors and mechanisms that regulate their mobilization. We describe a methodology for an in situ perfusion system of the mouse hind limb that permits direct quantification of stem and progenitor cell egress from the bone marrow. Progenitor cells are quantified by colony forming assays and immunohistochemistry. A strength of the methodology described is the ability to simultaneously quantify the mobilization of HPCs, EPCs and MSCs. Using this system we have shown that it is possible to achieve differential mobilization of these stem cell subsets using discrete combination therapies. Identification of such novel pharmacological regimens that stimulate the selective mobilization of EPCs and MSCs might be exploited in the future for tissue regeneration.