South African military officials say they are fighting a "human war" against the "formidable enemy" of HIV/Aids.
South Africa's armed forces are 'stretched'
Some 23% of South Africa's troops are infected with HIV - a similar rate to the adult population at large.
The army is taking part in a US-funded programme to see how Aids is affecting its combat-readiness.
This includes giving anti-retroviral drugs (ARVs) to some 1,000 soldiers. The government has been criticised for being slow to give ARVs to the public.
Some five million South Africans are HIV positive - more than any other nationality in the world.
"At this stage we do rise to the occasion as an organisation, but we are starting to get stretched," said Brigadier General Pieter Oelofse, director of medicine for the South African Military Health Service.
"We are a mirror-image of the population at large. We've got a challenge," he said at South Africa's second national Aids conference.
He said the army was getting "stretched" with its peace missions in Burundi and the Democratic Republic of Congo.
Under UN guidelines, HIV positive troops were not being deployed abroad, he said.
But Colonel Xolani Currie, commander of Project Phidisa, which is carrying out research on the effects of HIV on the military, said the ARVs were making a difference.
"We had members sitting hopelessly at the base with no hope," he said.
"Some of them are now running around in the mountains," he said, referring to HIV-positive troops now serving in border control units.