Voters have a choice of 27 candidates in the first election since last year's military coup upended one of the region's most stable democracies as Islamist militants hijacked a separatist uprising to seize a vast swathe in the desert north of the country.
The ballot opened at 8:00 am under heavy security after one of the main Islamist armed groups in northern Mali said Saturday it would "strike" polling stations.
"The polling stations and other voting places for what they are calling the elections will be targeted by mujahedeen strikes," the Movement for Oneness and Jihad in West Africa (MUJAO) said in a statement carried by neighbouring Mauritania's ANI news agency.
In a polling station at a school in Bamako, hundreds of voters had been queueing for more than an hour to cast their ballots.
"We are tired of bad governance. I'd urge the candidates to accept the results of our vote," said machine operator Kalifa Traore, 56.
Although the three-week campaign ended Friday without major incident, it played out in the shadow of violence in the north that has raised doubts over Mali's readiness to deliver a safe and credible election.
But Louis Michel, the head of the European Union observation mission, sounded a note of optimism Friday, saying conditions had been met for a credible first round.
"I believe that these elections can take place in a context and in conditions that are acceptable and do not allow for a distortion or an abuse of the result," he told reporters in the capital Bamako.
Much of the worry ahead of the polls has been focused on Kidal, occupied for five months by Tuareg separatists until a ceasefire accord allowed the Malian army earlier this month to provide security.
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