Most are homeless and jobless, part of a huge population of displaced people since the Soviet occupation of the 1980s, the civil war and Taliban rule that followed.
Few have access to testing, and those who do face being shunned by a deeply religious society that largely associates AIDS with sexual promiscuity and homosexuality - both taboo.
“One of the biggest challenges we have is that people believe HIV is found only among those who have ‘immoral’ relationships,” said Dr Fahim Paigham, head of Afghanistan’s National AIDS Control Programme.
Paigham runs the program out of a sparse port-a-cabin in the grounds of the Ministry of Health, a naked light-bulb and a photograph of President Hamid Karzai above his desk.
The inauspicious surroundings speak to the challenge of funding. Most comes from foreign donors such as the World Bank, which has spent $10 million over the past three years to fight HIV and AIDS.
“It’s not enough,” said Virk, “and it’s obviously very difficult to get donor interest in this because there are so many other issues.”
Health experts say they struggle to convince government officials in charge of prisons or counter-narcotics that they are not encouraging promiscuity or drug use by distributing condoms and clean needles.
A pilot project launched last year to provide methadone to drug users, taken orally as a substitute for injecting heroin, faces problems in securing supplies.
“There have been a few hiccups,” said Virk.
Prisoners are particularly vulnerable, crammed into over-crowded jails where drug use is rampant and access to clean needles and condoms limited.
One aid worker, who asked not to be identified, told the story of six prisoners, all drug users, who were transferred from a jail in western Farah province, bordering Iran, to Kabul in 2010. Once in the capital, they were tested for HIV, and all six were positive.
Health experts stress there are few cases of HIV within the sex industry or among truck drivers, often another high-risk group.
But studies suggest sex workers in Afghanistan know little about HIV, rarely use condoms and are unlikely to be tested for the disease.
“You know about the customs and culture of our country,” said Dr Tariq Suliman, director of the Nejat Center for drug rehabilitation and HIV/AIDS awareness.
“The people aren’t ready to talk about this issue.”
By Matt Robinson