Ruto, 46, charged with masterminding deadly post-election violence five years ago, is the most senior politician to date to face ICC judges, and his trial will start just days after Kenyan MPs voted to abandon the court in a world first.
He waved to the small crowd at the airport as he left, but made no comment.
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Fellow accused Joshua arap Sang, a radio boss accused of inciting and helping coordinate attacks during the violence, is already in The Hague, after flying there over the weekend. Both will plead not guilty.
Yesterday, Ruto prayed in church alongside President Uhuru Kenyatta, also accused of organising a campaign of murder, rape, persecution and deportation, whose ICC trial begins on November 12.
However, Kenyatta yesterday said that he will not allow both leaders to be away from Kenya at the same time.
"We will work with ICC, and we have always promised to do this," Kenyatta told a rally of supporters. "But it must understand that Kenya has a constitution, and Ruto and myself won't be away at the same time."
Kenyatta, who will also plead not guilty, said the "charges are false and will be dismissed".
"The plotters of this scheme will be named and shamed. The victory won't be Ruto's, Sang's or mine, but for Kenya," he said to cheering crowds.
Kenya's 2007 elections were marred by allegations of vote rigging, but what began as political riots quickly spiralled into a wave of ethnic killings and reprisal attacks, the worst violence in the country since independence in 1963.
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