Boycotts and isolated clashed have blemished Kenya's presidential election.
Violence has erupted in the opposition stronghold of Kisumu, one of four counties hit by violence.
Kisumu Governor Peter Anyang' Nyong'o, father of the Oscar-winning actress Lupita Nyong'o, said two people had been killed 29 people had been injured by police.
As a result, the electoral commission said voting would be postponed for the western counties of Homa Bay, Kisumu, Migori, and Siaya because of "security challenges". These areas are all likely to continue observing the opposition's boycott.
Though President Uhuru Kenyatta, who is seeking a second term, was declared the winner in an August vote, his victory was annulled because of "irregularities".
Opposition leader Raila Odinga has pulled out of the contest.
Mr. Odinga has said that the Independent Electoral and Boundaries Commission (IECB) failed to make the necessary changes needed to prevent a repeat of the mistakes that marred the earlier poll, although the IECB disputes this.
His opposition coalition - the National Super Alliance (Nasa) - made clear its participation in the election was contingent on reforms being made.
The electoral commission has seven days to declare the results.
After casting his vote in the town of Gatundu, Mr. Kenyatta urged people to cast their ballots so the country could move on.
"We're tired as a country of electioneering. It's time we moved forward," he said, adding that most of the country was "calm and peaceful."
Tens of thousands of police and other security staff were deployed to protect voters and polling stations.
About 50 people have been reported to have been killed in violence since Mr. Kenyatta was declared the winner in August's election.