In HIV infected persons, highly active antiretroviral therapy (HAART) has reduced both the morbidity and incidence of several disorders. Its effects on direct HIV-induced damage to the CNS remain controversial. In addition, HAART may provoke an “immune reconstitution inflammatory syndrome” (IRIS). Herein we report two patients who, despite HAART, developed a diffuse encephalopathy. Their clinical, radiological and neuropathological features are described. Immunohistochemical and PCR analyses were used to detect HIV and to exclude other viruses in brain tissue. The unusual inflammatory reaction in the brain tissue was defined by immunohistochemistry. Both patients had advanced HIV disease with low CD4 counts and high HIV “viral loads” before starting HAART. In both, HAART induced an increase in CD4 count and a marked reduction in HIV viral load, which was accompanied, in patient one, by worsening of pre-existing, and, in patient two, by development of, acute encephalopathy. At post-mortem examination, the brain of patient one showed HIV encephalitis. In addition, the brains of both patients revealed HIV-DNA by PCR, diffuse microglial hyperplasia and massive and diffuse perivascular and intraparenchymal infiltration by CD8+/CD4− lymphocytes. We suggest that the rapid immune reconstitution induced by HAART in these two patients led to a redistribution of lymphocytes into peripheral blood. This was followed by recruitment of CD8+ lymphocytes into the brain, which resulted in the diffuse infiltration described. The appearances in patient two further suggest that HIV brain infection, even without encephalitis, is sufficient to trigger this response.