Despite ongoing unrest in areas, President Omar al-Bashir -- wanted on war crimes charges related to the 13-year conflict -- has insisted voting go ahead on whether to unite Darfur's five states into a single region or maintain the status quo.
A united Darfur with greater autonomy has long been a demand of ethnic minority insurgents battling the Sudanese government since 2003, but they have boycotted the referendum, saying it is unfair.
The United States has also voiced concerns, warning that "if held under current rules and conditions, a referendum on Darfur cannot be considered a credible expression of the will of the people".
"All polling centres in Darfur's five states opened and no centre has encountered any difficulties," said Omar Ali Jomaa, head of the referendum electoral commission.
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"It is too early to assess the turnout."
The state's governor Abduwahid Yousif voted early at a small school serving as a polling station in an area mostly inhabited by government employees.
In its sunny courtyard, a line of around 100 women in brightly coloured headscarves waited in the early morning to vote inside classrooms temporarily transformed into voting booths.
"I voted for a single region, I want one region to solve Darfur's problems," the 38-year-old said outside the booth.
Searching for her name on a list of registered voters outside the health centre where voting was taking place, Samia Haroun said she supported a five-state system, the choice favoured the ruling National Congress Party.
"I want the five states, I want that choice to win," she said.
At other locations, only a handful of residents came to vote in the first hours of the referendum.
The vast western region has been mired in conflict since 2003 when ethnic minority insurgents rebelled against Bashir's Arab-dominated government over claims they were marginalising them.
Rebels have long demanded a return to the single-region system but say current unrest and the high number of people in camps for the displaced mean the vote will not be fair and are boycotting.