A simultaneous referendum was supposed to be held in Abyei on whether to become part of South Sudan but it was postponed due to conflict over demarcation and residency rights.

[10] It is envisaged that "popular consultations" in South Kordofan and Blue Nile, without a clear reference to referendums and/or independence, would raise concerns about the future of these regions.

In this case, a simple majority vote in favour of independence would result in secession for South Sudan;[14][15] should the turnout be insufficient in the first referendum, a second one will be held within sixty days.

Vice President Kiir acknowledged his administration had failed to deliver "the dividends of peace", and noted that a campaign to confiscate arms was a solution to maintaining stability.

[19] Sudan's President Omar al-Bashir said that the southern region had a right to choose to secede and that the referendum was helpful because unity "could not be forced by power."

Negotiations continue between the ruling parties in the north and south on potential post-referendum arrangements—looking at future issues such as citizenship, security, finance and wealth sharing.

"[25] Egyptian President Hosni Mubarak and Libyan leader Muammar Gaddafi later went to Sudan to try to assuage the conflict, though both men had previously called for the country to stay united.

[26] Member State of the Arab League Observers and key players feared violence ahead of the South Sudan referendum for a variety of reasons.

"[27] Didiri Mohammad Ahmad, an NCP official, said it was "not possible" to hold the referendum on the future of Abyei on time, and it could be delayed for months or be settled without a vote.

"[29] Sudan's UN ambassador Daffa-Alla Elhag Ali Osman told the Security Council that "It is evident that any attempt to conduct the plebiscite before achieving an acceptable settlement between the two parties [in Abyei] will mean only a return to war.

[31] The government Sudan asked the UN for the printing of ballots for the referendum as diplomats and the electoral commission warned of any further delay would miss the deadline to hold the election.

[33] Bishtina Mohammed El Salam of the Misseriya, who dominate the region along with the Dinka tribe, said he would not accept Abyei's seceding and joining the south even though the latter favored secession.

After the signing of the peace accord, some of the Nuba returned to the mountains, but the tribal elders refused to re-admit them into the tribes as they feared the abductees (mostly young men) were too Islamised.

[56] An early poll of 1,400 individuals was carried out by a coalition of civil society organisations in Southern Sudan prior to the January referendum, indicating that 97% of voters would likely vote for secession.

[58] The Youth and Sports Minister, Haj Majid Suwar, of the National Congress Party (NCP) suggested the government "may not recognise the results" and would "talk to ... the USA and the UN and the AU and say that the Sudan People's Liberation Movement didn't fulfill the CPA Comprehensive Peace Agreement" by allowing open campaigning and the withdrawal of their soldiers from southern areas.

Sudan's president, Omar Hassan al-Bashir, accused the SPLM of breaching the terms of the peace deal and warned of a return to conflict if the disputes were not settled before the referendum.

[72] Following concerns from the UN about delays, representatives of both regions affirmed a commitment to hold the referendum on time;[73] a media campaign was also launched to raise awareness and increase the turnout.

[75] In December 2010, the Constitutional Court agreed to carry out an investigation into a petition filed by local lawyers seeking the dissolution of the electoral body that was organizing the referendum.

An Al Jazeera English analysis said a few reasons for seeking secession were: a lack of expertise by post-colonial political elites in governing their respective countries and managing natural resources; the impact of the Cold War where many African countries took sides, rendering sovereignty ineffective; tribal prejudices and preferential service that dominate African politics; failure of governments to provide basic freedoms such as guaranteeing full citizenship for all.

As two important members of the African Union the latter two could be reluctant to support a new independent southern Sudan as a recognition thereof could "send a very clear message to these groups in their struggle for autonomy.

[89] The panel is composed of three senior officials, former Tanzania President Benjamin Mkapa, former Minister of Foreign Affairs of Portugal António Monteiro, and Bhojraj Pokharel, a former Chairman of the Election Commission of Nepal, who are appointed by and report to the UN Secretary-General.

Many of those who fled South Sudan during the civil war returned in the months and weeks leading up to the referendum, with some southern politicians trying to have them play a role in swinging the vote towards independence.

On 12 January, after three days of voting, representatives of the SPLA/M announced that, according to their estimates, the 60 percent turnout threshold required for the referendum's validity (corresponding to around 2.3 million voters) had been reached.

Some Canadian Sudanese have called for a boycott of the referendum, accusing the International Organization for Migration, which was tasked with operating the vote in that country, of "being influenced by the government in Khartoum.

"[103] Calgary-based journalist Mading Ngor of The New Sudan Vision dismissed these claims as "a conspiracy theory," adding "It's a very fragmented community here along tribal lines.

[105] Several days before voting began, the SPLA/M and a rebel faction led by Lieutenant General George Athor in Jonglei State agreed to a ceasefire agreement after nearly a year of fighting, meaning a halt to military operations, troop movement and recruitment by either side.

[108] As of 15 January, Radio France Internationale reported that the Sudanese central government in Khartoum had begun to recall ambassadors named by the SPLA as part of the CPA and had stopped shipping material for passports to Juba.

President of the United States Barack Obama said the result of the vote was "inspiring" as voters decided "their own future [and marked] another step forward in Africa's long journey toward justice and democracy".

[110] The precedence of the vote was seen as important because most African states' borders were decided during colonial times which resulted in a heterogeneous mix of religions, ethnicities, and cultures.

[115] The Minister of Cooperatives and Rural Development Jimmy Lemi Milla was shot dead in his office along with his bodyguard in an apparent personal feud.