A review was carried out of papers published between 1996 and 2006, documenting the introduction of highly active anti-retroviral therapy (HAART) in Brazil. Papers indexed in the MEDLINE and SciELO databases were retrieved using different combinations of keywords related to the management and care of AIDS in the post-HAART era: opportunistic diseases and co-infections, adherence to therapy, survival in the pre- and post-HAART eras, adverse events and side-effects, emergence and possible transmission of resistant viral strains, metabolic and cardiovascular disorders, and issues related to access to care and equity. The review documents the dramatic changes in HIV/AIDS disease progression in the post-HAART era, including an increase in survival and quality of life and a pronounced decrease in the episodes of opportunistic diseases. Notwithstanding such major achievements, new challenges have emerged, including slow evolving co-infections (such as hepatitis C, metabolic and cardiovascular disorders), the emergence of viral resistance, with consequences at the individual level (virological failure) and the community level (primary/secondary resistance at the population level), and impacts on the cost of new therapeutic regimens.