The continuous replication of HIV-1 in the central nervous system, in particular the brain, and its potential long-term deleterious effect is the focus of this review. Cognitive deficits are observed in a significant percentage of HIV-1-infected patients. That may occur despite successful peripheral suppression of the HIV-1 replication. Compartmentalisation of HIV-1 in the brain, genetic mutation of HIV-1, age, HCV coinfection and poor intracerebral penetration, as well as possibly a direct toxic effect of antiretroviral drugs, are factors that may account for potential creeping damage of the brain after many years of treatment. Patients with neurological symptoms or cognitive deficits may require another approach to the treatment of their HIV infection.