Opposition candidate Raila Odinga calls on his supporters to join him in boycotting the poll.
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Media captionKenya's election re-run explainedKenya will hold a controversial repeat presidential election on Thursday as planned, the head of the election commission has announced.
Uhuru Kenyatta, who is seeking a second term, won in August but the poll is being held again over irregularities.
Amid reports of unrest, he urged Kenyans to vote and remain peaceful.
Opposition candidate Raila Odinga has called on his own supporters to join him in boycotting the ballot, which he wants to hold later.
A bid to delay the election fell apart after only two out of seven Supreme Court judges showed up for a hearing.
One judge, Deputy Chief Justice Philomena Mwilu, failed to appear after her bodyguard was shot and wounded by unknown gunmen on Tuesday.
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The Supreme Court annulled the original election in August by a 4-2 majority, saying there had been "irregularities and illegalities".
Some international observers have reduced their involvement in the poll because they say the conditions are not conducive for a free and fair election.
There have been running battles between police firing tear gas and stone-throwing protesters in the city of Kisumu, an opposition stronghold.
Election commission chief Wafula Chebukati said the polls would open at 06:00 (03:00 GMT) after being given assurances by the authorities.
"Based on assurances given to this commission by the relevant authorities and security agencies... the elections as scheduled will go on tomorrow, 26 October 2017," said Mr Chebukati.
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Media captionPolice fire tear gas at protesters in KisumuBut he also complained of threats to the electoral commission's staff and said he could not guarantee their security while at work.
In a televised address, President Kenyatta said the security forces would ensure the safety of voters on Thursday.
Urging people to vote, he said: "Our forefathers fought and died for the right of the African to vote, we dare not reject this inheritance."
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Image caption Raila Odinga addressed supporters in NairobiIn a speech in Nairobi, Mr Odinga called for "free, fair and credible elections" within 90 days.
He said: "From today we are transforming the Nasa [National Super Alliance] coalition into a resistance movement."
"Do not participate in any way in this sham election," he told cheering supporters. "Convince your friends, neighbours, and everyone else not to participate."
Reversing an earlier call for massive demonstrations, he asked people to stay at home or pray because the government was a "bloodthirsty regime" which would "massacre" them.
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Earlier, Chief Justice David Maraga announced that a petition to delay the vote could not be heard because only two of the court's seven judges had shown up.
In addition to Ms Mwilu, one judge was said to be ill and receiving treatment abroad, another was out of the capital Nairobi and could not get a flight back, and two others were unavailable for undisclosed reasons.
The main opposition party says this is no coincidence and is a sign of the intimidation of the country's independent institutions, the BBC's Tomi Oladipo reports from Nairobi.
Where were the judges?
Image copyright AFPJudges who voted to annul August poll
Chief Justice David Maraga - present in court
Deputy Chief Justice Philomena Mwilu - absent. Her bodyguard was shot by gunmen on Wednesday
Justice Smokin Wanjala - absent. "Unable to come to court"
Justice Isaac Lenaola - present
Judges who dissented, saying results should be respected
Justice Jackton Ojwang - absent. "Unable to come to court"
Justice Njoki Ndung'u - absent. Missed her flight to Nairobi
On sick leave
Justice Mohamed Khadhar Ibrahim - receiving treatment abroad
The government had declared Wednesday a national holiday to allow people to travel to places where they were registered to vote.
Political tensions have sparked fears of unrest. After the 2007 poll, violence left over 1,600 people dead and thousands displaced.
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