Kerry met leaders of the Sunni Arab monarchy as part of a regional tour in which he has called for greater support for Syria's rebels but stressed that the United States ultimately wanted a political solution that includes all sides.
Saudi Foreign Minister Prince Saud al-Faisal told Kerry that Assad, a secular leader who belongs to the heterodox Alawite sect, has waged "unprecedented genocide" through the more than two-year conflict that has claimed nearly 100,000 lives.
"The regime's illegitimacy eliminates any possibility of it being part of any arrangement or playing any role whatsoever in shaping the present and future," he said.
Faisal also voiced dismay at the role of Iran, which has poured assistance to Assad to save its main Arab ally. Hezbollah, the Lebanese Shiite Muslim backed by Iran, has increasingly fought alongside government forces in Syria.
"Along with the regime's genocide against its own people, this adds an even deadlier element in the form of an all-out foreign invasion," Faisal said of Iran's role.
US policymakers have privately voiced concern that Saudi Arabia and fellow monarchy Qatar could embrace hardline Sunni guerrillas in strategically placed Syria if Western powers leave a vacuum.
Despite Faisal's stance, Kerry said that the United States supported an agreement last year in Geneva that would create a transitional government that includes both the rebels and regime, although not Assad himself.
"We believe that the best solution is a political solution in which the people of Syria have an opportunity to be able to make a choice about their future," Kerry said.
Saudi Arabia, while a longstanding US ally, practises a puritanical form of Wahhabi Islam. US officials have in the past voiced concern about money from Gulf Arabs funding Sunni hardliners in Afghanistan, Pakistan and elsewhere.
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