Our previous studies have demonstrated that mercury vapour exposure of Brown Norway rats induced an autoimmune response with development of glomerulonephritis and resulted in mercury deposition in the central nervous system, particularly in the neurons. The aim of this study was to investigate the effect on the central nervous system. A loss of Purkinje cells accompanied by Bergmann glial cell proliferation was found at a brain mercury level of 0.71 micrograms/g and became even more pronounced as the exposure dose increased. At a brain mercury level of 5.0 micrograms/g, a heavy gliosis was present in the brain stem, particularly around the pontine nuclei. In comparison with our previous study, the pathological changes in the brain appeared at the same mercury exposure dose as the glomerulonephritis. However, the location of pathological changes at the mercury level of 0.71 micrograms/g was not completely in accordance with the mercury distribution in the brain, which might be due to the sequence of mercury deposition, its amount or the vulnerability of the various cells classes.