Endothelial cells (EC) were isolated from brain, lung, and renal cortex using magnetic microbeads cross-linked to an antibody directed against the platelet-endothelial cell adhesion molecule-1 (PECAM-1). Levels of endothelial nitric oxide synthase (eNOS) and PECAM-1 were measured by Western blots and both were enriched in the positively selected EC fractions. The multidrug resistance P-glycoprotein (P-gp) was strongly enriched (59-fold) in the EC fraction from brain and was absent in the negative fraction, in which the glial fibrillary acidic protein (GFAP), an astrocyte marker, was present. Lower P-gp levels were detected in EC from renal cortex and lung. Reverse transcription-polymerase chain reaction analysis showed that the mdr1a gene was preferentially expressed in EC fraction from the brain. The mdr1b gene was found in EC from renal cortex whereas both mdr1 genes were detected in EC from lung. Our results indicate that EC can be isolated using microbeads and that the isoform of P-gp found in brain is mostly mdr1a, associated with EC.