The bloodshed stained Kenya's second presidential election in three months, worsening a fractious ballot that has been boycotted by opposition leader Raila Odinga and polarised east Africa's flagship democracy.
Two of the deaths occurred as protests raged in opposition strongholds in the west of the country, while the third person died in a Nairobi slum where clashes erupted between demonstrators and police.
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As voting drew to a close, election chief Wafula Chebukati made a televised address, saying the ballot would be postponed until Saturday in four protest-hit counties in the country's west: Kisumu, Homa Bay, Migori and Siaya.
The move, he said, was due to "security-related" challenges.
As Odinga's supporters hit the streets, others went to the polls to cast their ballots.
But, in stark contrast to the August election, several polling stations in key areas stood empty or welcomed only a handful of voters in an election likely to face more legal battles after its conclusion.
As voting headed to a close, police and hospital sources confirmed three people had been shot dead and at least 24 wounded, 11 of them by live rounds.
At Jaramogi hospital in Odinga's western stronghold of Kisumu, an AFP correspondent saw several people arriving covered in blood.
"This is crazy, they are shooting at us -- we are demonstrating and they shoot us!" said Samuel Okot, 20, who was sitting with his friend Joseph Ouma who had been shot in the knee and was howling in pain.
"What kind of country is this?
The violence drew a sharp response from rights watchdog Amnesty International.
"With tensions running high there is a very real threat of further bloodshed as the election re-run takes place," said Justus Nyangaya, director at Amnesty International Kenya.
"We are calling on the police to only use force as a last resort -- unlawful police killings and other human rights violations must not be allowed to recur."
In Kisumu, 19-year-old George Odhiambo died from blood loss after being shot in the thigh in clashes which erupted after protesters barricaded roads and polling stations to block the vote, police and hospital sources said.
Police said another man was shot dead in Homa Bay, also in the west, "where a large mob attacked a small police facility" prompting officers to open fire "to protect themselves," a statement said.
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