Calcium, a ubiquitous intracellular messenger, regulates numerous intracellular signaling pathways. To permit specificity of signal transduction and prevent unwanted cross-talk between pathways, sites of calcium entry in neurons are localized to specific membrane domains. To test whether Ca2+ extrusion pumps might exhibit analogous compartmentalization, we used immunohistochemistry to determine the subcellular localization of the two main plasma membrane Ca2+-ATPase (PMCA) isoforms in the cortex of the rat cerebellum. We find that both PMCA2 and PMCA3 are targeted to distinct compartments within the plasma membrane. In the molecular layer, both isoforms were at highest levels within synaptic profiles, but PMCA2 was postsynaptic and PMCA3 was presynaptic. Moreover, inside these compartments, both pumps exhibited nonuniform distributions. These data imply that cerebellar neurons possess remarkably effective mechanisms to target and restrict PMCA2 and -3 to specific membrane domains, raising the possibility that calcium pumps contribute to local Ca2+ signaling. J. Comp. Neurol. 500:1127–1135, 2007. © 2006 Wiley-Liss, Inc.