Liver carboxylesterase (CE) is an enzyme capable of metabolizing drugs, and may also function as a regulator of lipid metabolism. We examined two isoforms of CE (RH1 and RL1) by immunohistochemistry in rat brain. The anti-RL1 antibody did not stain any brain structures. The anti-RH1 antibody, however, stained oligodendrocytes in all brain tissues and tanycytes, as well as some neurons in the deep cingulate gyrus, various hypothalamic nuclei and the spinal trigeminal nucleus. In the central nervous system, rat CE may function as a protective factor against foreign chemicals in these glial and neuronal cells. The distribution differed from that of the homologous human isoform which has been previously found only in endothelial cells in human brain. A possible relation between RH1 positive neurons and the medial pain system is discussed.