We studied the central nervous system (CNS) of rhesus macaques during series of vaccination experiments in which attenuated simian immunodeficiency virus (SIV), SIVmac239Deltanef, was applied to the tonsils and the animals were later challenged with pathogenic SIVmac251 or SHIV/89.6P via tonsils or rectum. The pathologic lesions were graded on a scale of 0-5. The lesions were in general very mild, with a score of 0.5, except for one case, in which the animal had progressed to simian AIDS (SAIDS) and had severe lesions of grade 4. Except for the SAIDS case, the most common lesions were meningitis, ependymitis, inflammation of choroid plexus, and astrocytosis. Invasion of the challenge virus, SIVmac251, and pathologic lesions were detected 4 days post infection. The main features of the pathological lesions were similar during short-term follow-up (4 days to 2 weeks) and long-term follow-up (23 to 56 weeks) after challenge. No significant difference was found between unvaccinated controls infected with the challenge viruses and vaccinated and challenged animals. The pathological lesions in the one SAIDS case consisted of extensive lesions of the white matter in connection with confluent ependymitis, indicating an invasion through the choroid plexus. The lesions were characterized by a myriad of multinucleated giant cells of macrophage origin, which showed, together with individual macrophages, strong labelling for viral RNA and proteins. Productive infection of astrocytes was a very rare finding. In three cases infected via tonsils with SIVmac239Deltanef without challenge, we detected expression of Nef-derived peptides, indicating a selective pressure for Nef functions in the CNS.