At 8am on Sunday, voting began in south Sudan’s referendum to separate from the north. John Kerry, Jimmy Carter, Kofi Annan and the ubiquitous George Clooney are among the foreign dignitaries who have made their way to Sudan to observe the historic vote.

There were scenes of jubilation in Juba today as southern president Salva Kiir cast his ballot. But despite the result of the referendum seemingly almost certain before it began, it appears likely that this buoyant mood may soon be replaced with tension and impatience. The official outcome may not be declared for weeks.

In a country where many people may have to travel for days in order to vote, it was decided that the voting period should last for seven days. This is lucky because the turnout at many polling stations was so high on Sunday that people were told to wait overnight. Booths will not close until next Saturday. The actual counting of votes will not start until after polling is complete. The chairman of the Southern Sudan Referendum Bureau has said that official results may realistically have to wait until three weeks after counting begins.

While they wait South Sudanese may dwell on President Omar al-Bashir’s journey to the south last week where he made a speech strongly in favour of reconciliation whatever the outcome of the referendum. The positive message was highly welcome, but it is difficult to take Bashir entirely at his word. When you are accused by the International Criminal Court of orchestrating acts of genocide you lose a certain amount of credibility.

So far referendum related violence has claimed about nine lives this week, mostly in skirmishes between the SLRA and pro-Khartoum militias. It is a measure of the enormous possibilities for bloodshed that this relatively low death toll is actually considered a positive result. In the civil war which led to these events more than 2 million Sudanese were killed. If violence can be kept to its current level in coming weeks then the poll will be seen as largely peaceful.

Worryingly, some of the violence that has occurred has been in the oil rich district of Abyei, considered a historical bridge between northern and southern Sudan. A separate referendum was stipulated in the 2005 Comprehensive Peace Agreement to determine which new nation would be home to Abyei’s riches.  Unfortunately, negotiations on the final make-up of the Abyei poll broke down in recent months and the vote did not eventuate. Whatever the outcome of the wider referendum the future for Abyei remains unclear.

The regions of South Kordofan and Blue Nile are also areas that may prove to be catalysts for a wider return to violence. Both are located to the north of the proposed border. Both regions are predominantly Christian and fought on the southern side in the civil war. The potential for turbulence is clear.

Just a few months ago it seemed unlikely that this week’s referendum would occur at all. Preparations were massively behind and political will was lacking. The massive effort and focus required to get the main vote to occur on schedule has been an astonishing effort, but it has left the fate of some of the most disputed regions ambiguous. One thing though is certain — for now everyone will just have to wait and see what happens.