The perivascular (PVM) and meningeal (MM) macrophages form a distinct population of resident CNS cells, selectively expressing the mature macrophage marker ED2 in the rat. In order to elucidate the role of the PVM and MM in rats during normal functioning of the brain and pathology, we have developed a strategy employing a single intraventricular injection of clodronate liposomes. This resulted in a complete depletion of the PVM and MM. Clodronate liposomes did not deplete the microglial cells. In other parts of the body, a temporal and mild depletion effect was observed, which was restored within 1 week. Detailed analysis of the elimination and repopulation kinetics of the PVM and MM revealed a slow repopulation of the CNS, starting at 14 days post depletion. This selective depletion method of the PVM and MM will enable us to get direct insight in their functions during normal and pathologic conditions of the CNS.