To examine whether latent infection by HIV-1 occurs in the central nervous system, we optimized a procedure for amplification and detection of HIV-1 DNA in situ, in formalin-fixed brain tissue from a child with severe HIV-1-associated progressive encephalopathy and severe HIV-1 encephalitis. By the use of a two-step technique, which involved polymerase chain reaction with incorporation of digoxigenin-labeled nucleotides followed by in situ hybridization with biotinylated probes, we found infection of numerous mononuclear cells and astrocytes in the cerebral white matter as well as of perineuronal satellite cells in basal ganglia, but not of neurons. Following PCR amplification, nuclear signal was found in 10 to 20 times as many cells as in parallel, control experiments using conventional, unamplified in situ hybridization.