Interactions between ligands and cell surface receptors can be exploited to design adhesion-based microfluidic cell separation systems. When ligands are immobilized on the microfluidic channel surfaces, the resulting cell capture devices offer the typical advantages of small sample volumes and low cost associated with microfluidic systems, with the added benefit of not requiring complex fabrication schemes or extensive operational infrastructure. Cell–ligand interactions can range from highly specific to highly non-specific. This paper describes the design of an adhesion-based microfluidic separation system that takes advantage of both types of interactions. A 3-stage system of microfluidic devices coated with the tetrapeptides arg-glu-asp-val (REDV), val-ala-pro-gly (VAPG), and arg-gly-asp-ser (RGDS) is utilized to deplete a heterogeneous suspension containing endothelial cells, smooth muscle cells, and fibroblasts. The ligand-coated channels together with a large surface area allow effective depletion of all three cell types in a stagewise manner.