* Deputy president pleads not guilty in court
* Ruto on trial for post-election violence
* Trial sets stage for that of president in November
* Proceedings will test stability in Kenya and region (Adds defence response)
By Thomas Escritt and James Macharia
THE HAGUE/NAIROBI Sept 10 (Reuters) - Kenya's Deputy President William Ruto pleaded not guilty to crimes against humanity charges at the International Criminal Court on Tuesday, while back home Kenyans feared the case could reignite political violence they have struggled to overcome.
Ruto and co-defendant Joshua arap Sang are charged with orchestrating a post-election bloodbath five years ago, working with other conspirators to murder, deport and persecute supporters of rival political parties in Kenya's Rift Valley region.
Ruto's lawyer accused prosecutors of conducting a flawed and prejudicial investigation using tainted evidence and raised the possibility - not yet confirmed by judges or prosecutors - that this week's hearings would be adjourned because witnesses for the prosecution could not attend court.
Prosecutor Fatou Bensouda, in her opening speech, insisted the charges against the two men would stand.
"The crimes of which Mr Ruto and Mr Sang are charged were not just random and spontaneous acts of brutality," said Bensouda.
"This was a carefully planned and executed plan of violence ... Ruto's ultimate goal was to seize political power for himself and his party in the event he could not do so via the ballot box."
It is the first time such a senior serving politician has appeared in court to face international justice. Kenya's President Uhuru Kenyatta, Ruto's former rival and now his political ally, will also face trial on similar charges of crimes against humanity, beginning in November.
The court's public gallery was packed with dozens of Kenyan lawmakers and members of Ruto's family who had travelled to The Hague in a show of solidarity.
The cases have split public opinion, and witness testimonies of the violence in 2007-08 that killed more than a thousand people could re-open old wounds.
They are also a major test for prosecutors at the decade-old ICC, who have had a low success rate and face accusations of focusing on African countries, while avoiding war crimes in other global hotspots.
"One day there will need to be an inquiry ... into how on earth it happened that somebody not just not guilty but innocent came before the court to answer charges that have been shown to be patently false," said Karim Khan, Ruto's lead counsel.
Earlier, as the parties took their places in the courtroom, Ruto had appeared relaxed, laughing and smiling with his lawyers, while Sang gave the thumbs-up to a reporter.
Bensouda looked on impassively as Ruto's lawyer listed what he said were shortcomings in the prosecution's case.
Contrary to the prosecution's claim that Ruto, a Kalenjin, hated people of the Kikuyu tribe, his sisters were both married to Kikuyus, Khan said. And, he asked, how likely was it that Ruto had amassed a cache of guns and grenades under the eyes of the local Kikuyu police chief?
Khan played videos of interviews in which Ruto expressed support for the ICC's investigation and pledged to cooperate with the court despite describing the charges he faced as "something only possible in a movie".
Rival members of Kenyatta's Kikuyu and Ruto's Kalenjin tribes, wielding machetes, knives, and bows and arrows, went on the rampage after a disputed 2007 election, butchering more than 1,200 people and driving hundreds of thousands from their homes.
This year, Kenyatta and Ruto buried their differences and joined forces for another election, which was relatively peaceful. Their joint Jubilee Alliance ticket was elected in March after a campaign in which their supporters criticised the ICC for meddling in Kenya's affairs.
They say their new alliance makes violence unlikely. Their supporters say the court cases risk undoing years of painstaking reconciliation, though they insist the alliance will survive.
"LET JUSTICE TAKE ITS COURSE"
At the heart of the violence on Ruto's political turf in the lush Rift Valley town of Eldoret, some 300 kilometres (190 miles) north-west of the capital Nairobi, Patrick Muchiri said he watched the trial with several others crowded around a television at a restaurant.
"We would have wished that the cases don't take place since we have already reconciled, especially with our Kalenjin neighbours," said Muchiri, 53, a Kikuyu farmer who was evicted from his home near Eldoret by Kalenjin youth.
"But since the matter is before the ICC, let justice take its course. However, our concern is that this might create for us a big problem should they find Ruto liable. It would revive old wounds," said Muchiri, who lives at a tented camp near the town housing hundreds of displaced victims of the clashes.
In Naivasha, just north of Nairobi, where the worst revenge attacks by suspected members of a Kikuyu militia took place, Josiah Otieno, 34, a tailor, said a long wait for justice could soon be over.
"After years of waiting and suffering, we now believe that justice will be done, and those responsible for our problems punished," said Otieno, who said he was assaulted by militia who set his belongings ablaze.
Kenyan public backing for the ICC has slipped, however. An Ipsos-Synovate poll in July showed only 39 percent still wanted the trials to proceed, down from 55 percent in April 2012.
Khan laid the blame for what he said were prosecution failings on Luis Moreno Ocampo, Bensouda's predecessor, who he said had "latched onto an infected information stream" in his eagerness to indict suspects for the violence.
He said that, by depending on earlier investigations carried out by Kenyan prosecutors, the court had relied on a "drip-drip of evidence without regard to the fact that the source of the drops was a very tainted spring".
The horrors of the election violence shattered Kenya's reputation as one of Africa's most stable countries and dealt the economy a heavy blow from which it is only now recovering.
The charges also complicated relations between Kenya and Western leaders, who see Nairobi as central to the fight against militant Islam in East Africa.
Anger over the charges culminated last week when parliament voted for a motion calling for Kenya to withdraw from the international court's jurisdiction, though cases already in progress would continue. Kenyatta also threatened to suspend cooperation with the ICC if he and his deputy were summoned simultaneously, leaving no head of state in residence.
Judges said the cases would alternate at one-month intervals.
Both sides have been accused of intimidating or manipulating witnesses, allegations they deny. Khan, Ruto's lawyer, said claims of intimidation were designed to distract attention from a fundamentally weak prosecution case. (Additional reporting by Michael Kooren; Editing by Sara Webb and Will Waterman)