This protocol describes the use of immunopanning to purify endothelial cells from the rodent brain. Immunopanning permits the prospective isolation of endothelial cells from nervous tissue by relying on the binding of the endothelial cells to an anti-CD31 antibody adhered to a Petri dish. The cells are viable at the end of this gentle procedure, and they can be analyzed acutely for gene expression or cultured alone or in coculture with other central nervous system (CNS) cell types, including CNS pericytes and CNS astrocytes. This procedure can be used to isolate endothelial cells from either rat or mouse. We have suggested specific antibodies that work for each species. Note that endothelial cells from rats and mice have different morphologies; in general, rat CNS endothelial cells are longer and thinner than mouse CNS endothelial cells. This procedure can also be used to purify endothelial cells from different regions of the CNS, including brain and optic nerve. Dissociation procedures must be optimized for each tissue.