The 21 years of conflict that left at least 1.5 million dead and more than four million others displaced had the unintended benefit of restricting human movements and kept the spread of the virus in check, they say.
But now, they warn the combination of up to four million returnees, poor health and education services, cultural practices and 10,000 foreign UN troops has the potential to send southern Sudan's HIV infection rate soaring.
"With the arrival of returnees from Khartoum, AIDS is one thing that scares us," a UN official told reporters here last week.
Millions of returnees, poverty, poor health and education facilities, the low status of women and cultural practices such as female circumcision, polygamy and widow inheritance are potential ingredients for an HIV/AIDS disaster, the official said.
That threat is exacerbated by the presence of the peacekeepers who are to start deploying in July.
The UN official, who spoke on condition of anonymity, said there were fears of a repeat of the "Cambodia experience" where a massive 18-month UN operation was partly blamed for a shocking rise in HIV/AIDS in the early 1990s.
There are no reliable statistics on the region's infection rate although the ex-rebel Sudan People's Liberation Movement/Army (SPLM/A) says it is currently four to six percent.
Humanitarian agencies disagree and put the figure much higher, estimating the infection rate among SPLM/A fighters alone to be as high as 30 percent, a number the movement disputes.
Despite the differences, though, both aid workers and the SPLM/A agree that the potential for the spread of the disease in southern Sudan poses a major danger for the region.
"After the war, AIDS is the biggest enemy," SPLM/A leader John Garang said last year.
"The greatest health challenge for the New Sudan now is the increasing rate of infection of HIV/AIDS," the Catholic Diocese of Rumbek said in its 2005/06 handbook.
Here in Rumbek, the dilapidated provisional capital of the south, posters raising HIV/AIDS awareness have been plastered across bullet-scarred walls throughout the town.
But officials say that promiscuity and intravenous drug use are on the rise and that most young southern Sudanese believe AIDS affects only neighboring states like Kenya and Uganda, both of which will contribute troops to the UN peacekeeping mission.
Of equal concern is the polygamy tradition among the majority Nilotic Dinka and Nuer tribes in southern Sudan which could play a part in fueling infection rates, they said.
"It is very hard to convince these tribes that this practice will spread AIDS," said a Kenyan nurse working in a Catholic mission hospital in the town of Old Fangak northwest of Rumbek.
"Coupled with malnutrition, it is going to be catastrophic if the virus actually takes root," another medical worker in southern Sudan's Bahr el-Ghazal region told AFP.