We quantitated the brain viral burden in autopsy material from AIDS patients with and without HIV encephalitis. Central nervous system (CNS) samples from 45 AIDS autopsies with less than 48 hours postmortem autolysis and without significant non-viral opportunistic infections were analyzed using immunocytochemistry (ICC), antigen capture assay (ACA) and polymerase chain reaction (PCR). Approximately three-quarters of the cases contained HIV DNA by PCR. The majority of these had abundant gp41 detected by ICC, but approximately one-third had no HIV p24 detected by ACA. With all assays, HIV proteins and DNA were most abundant in deep gray matter. Approximately one-quarter of the cases contained HIV p24 by ACA in both CNS tissue and cerebrospinal fluid. In more than half of the cases cytomegalovirus was detectable in the brain by PCR, however, only in the basal ganglia of one case was human herpes virus-6 detectable by PCR. In conclusion, HIV infection of the CNS was observed in the majority of AIDS autopsies, however, the quantity of virus was variable between cases and within different neuroanatomical regions. Differences between the quantitation methods could be either technical or biological, however, any of them could be used to compare assessment of HIV burden by different laboratories.