Among the victims of Sudan's conflict were 27,000 boys orphaned by the fighting. Known as the Lost Boys, some were forced to fight as child soldiers, while others fled and became refugees.
An estimated 1.5 million people were killed and another four million were displaced in what became Africa's longest-running conflict.
The refugees fled to camps in Ethiopia and other neighbouring countries.  It was a dangerous journey - many drowned or died from hunger. Others were killed by wild animals. Some of those who survived ended up far away, in countries such as the US.
More than two decades of fighting ended in a peace deal in 2005 which led to the people of South Sudan voting for secession in a referendum.
As the new nation starts building its future, three of these Lost Boys have told their stories to BBC Two's This World, speaking about what independence means to them and their hopes for the future.
Along with about 4,000 other Lost Boys, Kuol Awan was resettled in the United States in 2000.
The 32-year-old has been living in Arizona, managing the Arizona Lost Boys' Centre. It is the largest centre of its kind, helping its 600 members to adjust to life in the US.
Independence for South Sudan provided a chance for Mr Awan to return to the country of his birth.
He wanted to revisit the village that was his home until the age of eight and which he had not seen since. He was keen to search for any relatives who may have remained.
But much had changed. Shortly after he left, the village was burnt to the ground and people have only recently returned to rebuild their homes.
"It used to be a very close village. The way I left it is not the way it is [now]," he says.
Mr Awan tried to visit his mother's grave to pay his respects, but it had been buried in the sand and he was unable to find it.
"It's hard to kind of conceive. Where I used to play and see my family, now nobody is here," he said.
"I feel like someone who has been away from home for a long time."
He feels that independence promises a new start and a chance to make the country peaceful and prosperous.
Lam Tungwar was recruited into the rebel Sudanese People's Liberation Army (SPLA) when he was seven years old. He was promised an education, but instead he was taught how to fight.
"I didn't know why I was fighting. No-one could answer me," said Mr Tungwar. "I learned a different lesson, a lesson of war, a lesson of death, a lesson of killing people."
Today, he is one of South Sudan's biggest pop stars. He was heavily involved in organising some of the cultural events staged to celebrate independence.
He wants to put his own past behind him and believes the country should do the same.
"We are tired of being oppressed. We're tired of our dignity not being recognised. We still have a lot to do ahead, to show our joy to the world."
Mr Tungwar is optimistic that secession will bring new responsibilities and opportunities, a chance for the country to define itself.
"We need to start working. The whole world will not give us aid."
"Maybe we'll be the food basket of Africa, or maybe we'll be the good example for the democrats in Africa."
Paul Manyok has lived in exile in Nashville, Tennessee, where he helped to transport hospital patients for medical tests. He also worked in a cafeteria and as a salesman.
He was granted US citizenship when he arrived, but feels he is both American and Sudanese. Like Mr Awan, he is involved with a community centre for Lost Boys and wants to keep Sudanese oral history and culture alive.
But he is still haunted by the day his village was attacked.
"The time they came, they burned houses, a lot of my relatives were killed," he said.
"People are running like crazy, we could hear people crying everywhere."
With a degree in political science and Bible studies, Mr Manyok wants to give something back to his new country, South Sudan.
"I would love to transfer the skills, knowledge, values and attitude that I've learned in peace-building and conflict resolution.
"I think with that I can bring some respect to Southern Sudan," he said, "and of course, a young nation will require young leaders that might help the generation that have sacrificed so much."
BBC Two's This World: Return of the Lost Boys of Sudan will be broadcast on Monday 12 December 2011 at 19:00 GMT. Or watch online (UK only) via BBC iPlayer at the above link.
When South Sudan was created as an independent country in July, it offered a new hope and possibilities for a whole generation whose childhood was blighted by civil war.