Many of the boys came from the predominantly Christian southern section of Sudan who were fleeing persecution by Muslims that dominated northern Sudan. The name was given by aid organizations, including the International Rescue Committee program which resettled some of these refugees from Sudan to the United States.

In 2001, about 3801 Lost Boys arrived in the United States, where they are now scattered in about 38 cities, averaging about 100 per city.  Halted after 9/11 for security reasons, the program restarted in 2004, but peace talks were underway in Sudan, and so other refugee crises in other countries took priority.  As of 2006, the largest population of Sudanese refugees in the United States is in Omaha, Nebraska which hosts about 7,000 people.  A variety of charities helped bring Sudanese refugees to the United States, such as Catholic Charities. A variety of programs have been done to help and understand these displaced people, everything from reconnecting to their traditional dancing to dental work to replace teeth which had been removed by traditional custom, but whose loss is negative in the USA.

Most of the boys were orphaned or separated from their families when government troops systematically attacked villages in southern Sudan killing many of the inhabitants, most of whom were civilians.  The younger boys survived in large numbers because they were away tending herds or were able to escape into the nearby jungles.  Orphaned and with no support, they would make epic journeys lasting years across the borders to international relief camps in Ethiopia and Kenya evading thirst, starvation, wild animals, insects, disease, and one of the most bloody wars of the 20th century.  Experts say they are the most badly war-traumatized children ever examined.