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NAIROBI, Kenya — He has been charged with heinous crimes, accused of using a vast fortune to bankroll death squads that slaughtered women and children. His running mate also faces charges of crimes against humanity, and as Kenya’s election drew closer, the Obama administration’s top official for Africa issued a thinly veiled warning during a conference call, saying that Kenyans are, of course, free to pick their own leaders but that “choices have consequences.”

But when the ballot counting began this week, Uhuru Kenyatta, the son of Kenya’s first president, surged ahead in the race for president and stayed out front as the margin narrowed early Friday. Soon, the Obama administration and its allies could face a tough choice, made even more complicated by the appearance of taking sides against a candidate who might win.

Does the United States put a premium on its commitment to justice and ending impunity — as it has emphasized across the continent — and distance itself from Kenyatta should he clinch this election?

Or would that put at risk all the other strategic U.S. interests vested in Kenya, a vital ally in a volatile region and a crucial hub for everything from billion-dollar health programs and U.S. corporations to spying on al-Qaida?

Even the little things could be tricky. Are the U.S. diplomats who interact with the Kenyan government on a daily basis not supposed to shake Kenyatta’s hand? What about sharing a dais with him? The British have already stated that they would avoid any contact unless it was essential.

“This is going to pose a very awkward situation,” said Jendayi Frazer, a former assistant secretary of state for African affairs. “Kenyatta knows he needs the United States, and the United States knows it needs Kenya.”

U.S. officials have declined to discuss publicly what a Kenyatta victory would mean, and several reiterated the rather anodyne video message from President Barack Obama in February, in which he said, “The choice of who will lead Kenya is up to the Kenyan people.”

But Johnnie Carson, the top administration official for Africa, was not quite so diplomatic when he repeatedly warned soon after that “choices have consequences,” which critics say backfired by energizing supporters of Kenyatta and his running mate, William Ruto, driving many to the polls to rally behind them.

“When you inject yourself into an election,” Frazer said, “you never know how it will play.”

Carson responded, “One comment does not swing a contest.”

If he wins the presidency, Kenyatta, who was leading with about 48 percent of the vote early Friday, would become the second African head of state after Sudan’s Omar al-Bashir to face grave charges at the International Criminal Court at The Hague. But that does not mean he will meet the same diplomatic isolation as Bashir, who is wanted on an arrest warrant and cannot travel to much of the world.