HIV, which attacks the body's natural defences, also damages the brain, three dimensional medical scans have shown.
The MRI images captured by a US team could show why up to 40% of people with HIV/Aids have neurological symptoms.
Compared with healthy people without the virus, the brains of the Aids patients studied were 15% thinner.
Scans could be used to spot patients who might benefit from brain-protecting drugs, the authors told Proceedings of the National Academy of Sciences.
HIV experts said more work was needed to check that neuroprotective drugs would be beneficial to Aids patients and that these treatments would not be safe to take alongside the powerful anti-HIV drugs such individuals are already on.
As drugs improve, people with HIV/Aids are living much longer.
However, at least two in five living with HIV/Aids will suffer from cognitive impairments, ranging from minor deficits to dementia, studies suggest.
While researchers are aware of this, the pattern of damage the virus causes in the brain has not been well understood.
Dr Paul Thompson, from the University of California, Los Angeles, along with colleagues from the University of Pittsburgh, used 3D magnetic resonance imaging (MRI) scans to see what was going on in the brains of 26 patients with Aids.
Compared with 14 healthy controls, the Aids patients had 10-15% thinner brain regions, including areas called the primary sensory, motor and premotor cortices, regardless of whether they were taking anti-HIV drugs or not.
This tissue loss shown up by the brain mapping correlated with the cognitive and motor deficits that the Aids patients displayed on a battery of brain function tests.
The brain tissue loss was the opposite of that seen in common dementias such as Alzheimer's disease and appeared to be related to the individual's CD4 count - a marker of how far HIV/Aids has progressed and how healthy the person's immune system is.
The researchers said: "With 40 million patients worldwide now living with HIV/Aids, detailed biomarkers of [brain] deficits, such as the cortical maps presented here, are increasingly needed to help gauge the success of neuroprotective therapies.
"Here, they reveal how Aids impacts the brain and may also help identify early changes in neurologically asymptomatic patients with HIV who might benefit most from neuroprotective agents."
Rod Watson of the Terrence Higgins Trust said: "We do know that some people with HIV could go on to develop Aids-related dementia or other illnesses affecting the brain.
"This study tracking any cognitive decline is interesting but small. We'd need more solid evidence on how HIV can affect the brain in different individuals before we looked at offering neuroprotective drugs.
"In particular, there would have to be detailed research into how useful these drugs would be and how safe in terms of interacting with existing HIV treatments."
David Simpson, professor of neurology at Mount Sinai Medical Center in New York, told the BBC News website: "This paper is interesting and provocative, and if the value of this technique is validated in other studies, from other centres, this imaging approach may be a valuable surrogate marker of brain function in HIV infection."
He added: "The increased survival of patients with HIV, due mostly to HAART, has placed greater emphasis on long-term issues affecting quality of life, such as neurological disease."
Professor Simpson said that, while many neurological complications are more common in advanced Aids, others, including HIV-associated cognitive disorder, may occur in HIV positive people who have relatively high CD4 counts.
Steve Small, deputy chief executive of Mildmay, an HIV/AIDS charity, specialising in HIV related brain impairment in the UK, said: "This research backs up what most people have known for sometime.
"You have an increased propensity for cognitive decline the more immunosuppressed you are but, whereas before we have thought that this would go away with anti retro virals, this study claims that it will not."