Microfluidic cell separation systems have emerged as attractive alternatives to traditional techniques in recent years. These systems offer the advantages of being able to handle small sample volumes and at the same time achieve highly selective separation at low cost. Microfluidic devices with surface-immobilized adhesion molecules can achieve separation by exploiting ligand-receptor interactions. When ligands are immobilized on the microfluidic channel surfaces, the resulting cell capture devices offer the typical advantages associated with microfluidic systems, with the added benefit of not requiring complex fabrication schemes or pre-processing incubation. This presentation will describe how a microfluidic system of devices coated with peptides can be utilized to deplete a cell suspension of endothelial cells, smooth muscle cells, and fibroblasts in order to isolate a fourth cell type by negative selection. The peptides utilized are arg-glu-asp-val (REDV), val-ala-pro-gly (VAPG), and arg-gly-asp-ser (RGDS). Separation is achieved by continuous flow and by the provision of large surface areas for cell attachment. The significance of this approach is that it can be utilized to isolate stem and progenitor cell populations from digested tissue as a precursor to conventional tissue engineering on scaffolds or cell-based regenerative therapeutics. Furthermore, this approach could be an effective way to isolate stem/progenitor cells whose markers are not fully characterized.