Prosecutors say Deputy Prime Minister Uhuru Kenyatta masterminded "one of the most violent periods in Kenya's history" in 2007-08 in which more than 1,000 people died in the wake of disputed elections.
International Criminal Court presiding judge Ekaterina Trendafilova said, "Our duty is to distinguish between those cases which should go to trial or not on the evidence provided," as the court hearing opened in The Hague.
"The confirmation of charges hearing is not a trial before a trial, nor is it a mini-hearing," she said, adding: "The suspects are considered innocent until proven guilty."
A potential presidential candidate in 2012, Uhuru Kenyatta, 49, is the son of Kenya's founding father Jomo Kenyatta.
Kenyan President Mwai Kibaki's right-hand man Francis Muthaura, 64, and ex-police chief Mohammed Hussein Ali, 55, are also facing charges for their part in the violence. The three men remain free.
Supporters of Kibaki's Party of National Unity (PNU), they are suspected of devising and implementing a "common plan" to attack rivals of then opponent and now Prime Minister Raila Odinga's party.
The three men allegedly used a Kenyan criminal organisation called the Mungiki and party youth to keep the PNU in power "by all means necessary."
The ICC prosecutor's office said 1,133 people died and more than 663,000 others were displaced after clashes between the rival supporters, when political riots turned to ethnic killings, sparking further reprisals.
The hearings, during which prosecutors will try to convince the court they have enough evidence to go to trial, are scheduled to run until October 5.
The three are a second group of senior Kenyans to appear before the Hague-based court after ICC prosecutor Luis Moreno-Ocampo in December 2010 asked judges to issue summonses against them for crimes against humanity.
"We hope that our intervention would help. We hope that we can start a new rule, a rule that says that leaders cannot commit atrocities to gain power or to remain in power," Moreno-Ocampo told journalists during a briefing shortly before the hearing started.
Earlier this month ex-Kenyan ministers William Ruto and Henry Kosgey, as well as radio executive Joshua arap Sang, also appeared before the court to determine if they should stand trial for their part in the violence.
Supporters of Odinga's Orange Democratic Movement (ODM), they are accused for their part in attacks on PNU members in the Rift Valley. They all protested their innocence and the court's decision is still awaited.
Kenya last month lost an appeal to stop the ICC from trying the six men, with the court turning down a request to have them in the dock in Nairobi.