Some 6 million Guineans are expected to vote for eight candidates at more than 14,800 polling stations watched by anti-riot police, gendarmerie and international observers.
It is this West African country's second democratic presidential election in more than 50 years.
Guinea endured decades of corrupt dictatorship after its independence from France in 1958. In 2008, after the longtime strongman died, a military coup led to tumultuous rule until the junta's leader agreed to go into exile.
President Alpha Conde later won the country's first-ever democratic election in 2010.
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Similar violence this week killed at least three people and injured some 50.
Conde voted in the Boulbinet neighborhood in Conakry's center where he and other Cabinet ministers live. "I call on each Guinean to vote in acceptance of the other and in calm and tranquility," he said.
Diallo voted in the Dixinn area of Conakry. "I call on Guineans to elect the best. I invite the community to help Guinea preserve peace. We must ensure this election is transparent," he said.
In Yembeya, a neighborhood on the periphery of the capital, voters who had been lining up since 6 a.M. Local time were not able to vote until after 10:30 a.M.
In Bambeto, election official Idrissa Balde said that some stations would stay open until at least 8:00 p.M. To allow everyone to vote.
Other polling stations in Conakry seemed to have all the needed materials. Mamadou Bhoye Diallo, an opposition supporter, said he voted with melancholy.
"With these irregularities, I am convinced that it is lost for my candidate," he said of main opposition candidate Diallo.
In Sierra Leone, voting by nearly 16,000 Guineans was canceled Sunday because election materials did not get to the Guinean embassy in time to be distributed, said the head of the Guinean elections team, Razeh Sao Kpoghomou.