There was made an attempt to link interdisciplinary research methodically, from clinical diagnostic techniques, modern instrumental, laboratory and basic research to their implementation in practice. The experience of several partner groups studying the brain in HIV infection was analyzed and summarized. It was based on an interdisciplinary approach, the goals and authorities of infectious disease specialists, psychiatrists, neurologists, radiologists, laboratory doctors, clinical examination algorithm, the role of history and interview, express-diagnostic of cognitive functions, specialized psychiatric, neurological diagnosis, conclusion of clinical psychologists, indications for radiology methods. The choice and analysis of radiological and instrumental methods, the volume and structure of laboratory methods of central nervous system study were justified. The role of molecular genetic studies of HIV in blood and cerebrospinal fluid, the identification of drug-resistant forms of the virus was determined when choosing the therapy.