Objectives (1) To determine whether detection of HIV proviral DNA sequences in the cerebral cortex correlates with the presence of pathological changes in this region, believed to contribute to the HIV-associated cognitive motor complex. (2) To compare the frequency with which HIV infects cortical and subcortical regions of the brain. Design In vitro studies on HIV neurotoxicity suggest that HIV may be involved in the pathogenesis of cortical damage, recently defined as diffuse poliodystrophy (DPD) in AIDS. Previous detection of HIV antigen has localized HIV more frequently to subcortical than to cortical regions It is not known whether HIV preferentially infects subcortical tissues or if viral expression varies in these two regions. Methods HIV antigen and proviral DNA sequences were detected in anterior frontal lobe tissues using immunohistochemistry (IHC) and the polymerase chain reaction (PCR), respectively. DPD was assessed by staining with antibodies against astrocytes (CFAP) and microglia/macrophages (HAM 56). Results HIV proviral DNA was detected in nine out of 15 cortical samples and in 10 out of 15 white matter samples, whilst HIV p24 antigen was localized to the cortex in three out of 15 and to the white matter in seven out of 15 cases. DPD was found in 10 cases, although in five a different aetiology may have been involved. However, DPD was present in eight out of the nine cases in which HIV proviral DNA was detected in the cortex. Conclusions Using a non-isotopic PCR method, HIV was detected in the brains of more cases than would be expected on the basis of IHC detection, and was present in the cortex as frequently as in the white matter. HIV, together with other factors, may contribute to the pathogenesis of DPD.