The conflict, in which about 1.5 million people were killed, pitted the Muslim-dominated government in Khartoum against the mainly Christian and animist south.
January's breakthrough peace deal included wealth and power-sharing arrangements, created a national unity government in Khartoum and gave southern Sudan a six-year period of autonomy after which it will hold a referendum on secession.
But peace - or what passes for it - has not stopped the exodus. Fighting continues in Darfur, where conservative estimates put the number of deaths at 200,000.
In Sudan's now comparatively peaceful south, cattle herders and children carry AK-47s, tribal war is common and the few passable roads are littered with landmines.
Although the devastating 21-year conflict ended with the peace agreement between the ex-southern Sudan rebels, the Sudan People's Liberation Army, and the Khartoum government, militia still roam. Uganda's Lord's Resistance Army (LRA) also launches sporadic attacks through its cells in southern Sudan, disrupting relief efforts.
This year was meant to be the first year of stability for Africa's biggest country but if the figures at Kakuma refugee camp across the Kenyan border are any indication, an alarming number of Sudanese are still choosing exile.
In the first 11 months of official peace, 7000 Sudanese more than three times the number in previous years - have sought refuge at Kakuma, East Africa's isolated, violent, halfway house and one of the world's oldest and biggest refugee camps. Last week, the camp was home to 91,000 refugees, a record high.
"We can cope now, but we will not be able to cope if we get many more," an aid worker said. "They should not be coming here now, it should be the other way around.
Simon Juma, 26, who fled to Kakuma from southern Sudan two months ago, said the reason was simple. "They say there is peace, but there is no peace in south Sudan."
He wanted to get an education at Kakuma and then maybe move somewhere else, he said.
"How do I get to Australia?" he asked, leaning up against one of the tiny mud shelters that dot the 25-kilometre stretch of Kakuma. "Where do I apply?"
Other refugees, encouraged by United Nations agencies to return home, hope they can rebuild their lives in southern Sudan. Achol Nyang, who fled from the fighting to Kakuma in 1997, was preparing to return home with her three children, all of whom were born in Kakuma.
She thinks she is between 26 and 28 but, like many in the camp, she has no records. She only remembers fleeing the civil war, between the Muslim north and the Christian south. "We ran to the bush but we didn't have food and water," she said.
A few days later she and her children flew to Bor on a chartered UN World Food Program plane in the first organised repatriation of refugees since the peace agreement was signed.
The day before she flew out, Achol had had her hair done. "It is like when you go somewhere, you want to look sharp," she said. "I'm scared because I don't know what will happen. Maybe I will starve or there might be some other problem."
Her concerns about what awaits her in Bor are shared by others at Kakuma, most of whom are refusing the voluntary repatriations being offered by the UN.
Simon Crittle, a spokesman for the World Food Program, said people would leave then they felt the conditions were right. "[Then] we expect a flood," he said.
The assurances of the aid groups were enough to convince 40-year-old Abuoi Aguto Ngok to travel to Bor last week. But he went alone, leaving behind his pregnant wife and their four children. He wanted to make sure his homeland was safe.
" I came to Kakuma to get food and medical help," he said. That was 13 years ago. "The region was not good. The people are not in good moods. That's why I am going alone, to see the situation first," he said.
The official repatriation is expected to take five years. Aid groups are trying to be optimistic but even the UN admits that instability in the region could see refugees who have lived two decades in exile move from one crisis into another.
When the first planeload of returnees touched down in Bor last Saturday, there was no fanfare, no official welcoming party and very little to indicate the historic nature of the flight or the political significance of the people on board.
The 14 families who stepped onto the dusty ground of southern Sudan were the first in what the UN has dubbed one of the biggest and most important refugee operations in history.
Refugee workers in Bor also are candid about their concerns about whether the return was premature. Earlier a dispute in Bor between a 22-year-old student called Makur and his Arab flatmate erupted into a violent race riot. Terrified UN staff, who had only moved into the town three weeks earlier, locked themselves into their compound.
Makur, who was stabbed in the chest, back and head, is recovering in the region's hospital, a run-down building with no running water and no electricity and where soft-drink bottles were being used as makeshift drips. " People are still hostile. Anything, even something small, can trigger violence," Dr Benjamin Malek Alier, a surgeon, said.
The region's newly-appointed health minister, Agot Alier Leek, toured the hospital.
"This is Africa. It is south Sudan. This happens. You have a population that is coming out of war," he said.
The ethnic tensions and the town's lack of even the most basic resources provide a disturbing backdrop to the returning refugees. In addition to the UN flights, more than 6000 refugees have arrived in Bor under their own steam in the past weeks, doubling the poverty-stricken town's population.
The former garrison town, still has a big military presence. SPLA officers march in the town centre while a northern army battalion is camped on the outskirts.
"Danger, danger!" a soldier yelled, gesturing away from a spot on the edge of the River Nile.
Locals explained later that northern soldiers used to kill rebels there and feed them to the crocodiles. The crocodiles now lurk in the area waiting for food.
The return of thousands of refugees is expected to make the situation worse. There is no sewerage system, no phone network, no electricity and no water.
Dr Alier is to return to Nairobi in January, leaving Bor's only hospital without a surgeon at the time when the strain on health resources is set to skyrocket.
Just a week after the UN flew in those first refugees the situation has deteriorated.
A dispute at the landing strip being used by the UN broke out on Wednesday night between a SPLA lieutenant colonel and a militia member which escalated into a shootout, ending with the officer's death.
And two months ago, two UN workers involved in landmine clearance were killed and two Sudanese soldiers wounded when their convoy was ambushed as it returned to base camp. The shootings are believe to have been carried out by the LRA. But the Khartoum government, which once supported the LRA but now allows Uganda to chase the rebels across the border, denies it.
Before the attack on the landmine engineers the UN had already cleared 640 kilometres of roads in the Juba area, destroying more than 2800 anti-personnel and anti-tank mines. A year after the end of the civil war, this also will be the first time in decades that Christians in the south can freely celebrate Christmas.
It should also be the time when they put down their weapons. But in a country where for 50 years arguments have been settled at the point of a gun, the tools of conflict resolution are still brandished openly. A semi-automatic weapon in Sudan goes for the same price as a cow and is just as common, often found in the hands of children.
Oxfam
www.oxfam.org.au
or 1800 034 034.
Red Cross Australia
www.redcross.org.au
or 1800 811 700.
UNICEF Australia
www.unicef.com.au
or 1300 134 071.