Opposition leader Raila Odinga, who has pulled out of the election re-run, has called on his supporters to boycott it.
Mr Kenyatta was announced the winner in an 8 August vote but the poll is being held again because of "irregularities".
The polls on Thursday opened at 06:00 (03:00 GMT) with tens of thousands of police and other security personnel deployed to protect voters and polling stations.
One voter in Nairobi's Mathare slum, taxi driver David Njeru, 26, told the AFP news agency: "It is my duty to vote. Last time the queue was all around the block and I waited six hours to vote, this time the people are few."
On the eve of the vote, Mr Kenyatta urged people to cast their ballots: "Our forefathers fought and died for the right of the African to vote, we dare not reject this inheritance."
As the polling stations opened their doors, opposition protesters attempted to block roads in parts of Nairobi's Kibera slum, with riot police using tear gas in a bid to disperse the crowds.
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