Na(+)-independent K(+)-Cl(-) cotransporters function in the regulation of cell volume, control of CNS excitability and epithelial ion transport. Several K(+)-Cl(-) cotransporter isoforms are expressed in the nervous system, and KCC3 in particular is expressed at significant levels in both the brain and spinal cord. The cellular localization of this transporter has, however, not been determined. In this study, we generated a polyclonal antibody against the KCC3 cotransporter in order to characterize and localize this protein in the brain. Western blot analysis of mouse kidney and brain demonstrated KCC3 proteins of different size, 150 and 170kDa, respectively; this disparity remained after deglycosylation. Northern blot confirmed the presence of two distinct forms of KCC3, KCC3a and KCC3b, generated by the inclusion of different first coding exons. KCC3a predominates in the brain, whereas KCC3b is more abundant in the kidney. Western blots with membrane protein from dissected mouse brain revealed abundant expression in all brain regions examined: the cerebral cortex, hippocampus, diencephalon, brainstem and cerebellum. The spinal cord showed the highest levels of KCC3 expression, whereas peripheral nerves did not contain immunoreactive KCC3 protein. Western blot analysis of whole brain from rats of various ages indicated increasing expression in the postnatal period, concurrent with CNS maturation and myelination. Immunofluorescence studies demonstrated strong signal in myelinated tracts of the spinal cord, consistent with individual myelin sheaths. Brain sections also showed white matter enhancement, but also cellular signal consistent with pyramidal neurons and Purkinje cells. The base of the choroid plexus epithelium was also strongly labeled. These data demonstrate the specificity and diversity of KCC3 expression in the mouse CNS.