The United States has asked the Islamic group that controls the Somali capital to hand over three men accused of links to the 1998 US embassy bombings.
The Islamic courts control much of southern Somalia
Senior US diplomat Jendayi Frazer said the alleged "terrorists" were from the Comoros Islands, Kenya and Sudan.
Somalia's Union of Islamic Courts has repeatedly denied accusations that it is harbouring foreign Islamic fighters.
The call comes as the Islamic courts are holding talks with Somalia's interim government in Sudan.
Correspondents say the request is a u-turn for the United States, which is widely believed to have backed an alliance of warlords, which was defeated by the Islamic courts in Mogadishu earlier this month.
Ms Frazer, Assistant Secretary of State for African Affairs, said there were many "foreign terrorists" in Somalia but the three most wanted by the US were:
- Comoran Fazul Abdullah Mohammed
- Kenyan Saleh Ali Saleh Nabhan
- Sudanese Abu Taha al-Sudani
She said they had been involved in the 1998 bombings of the US embassies in Kenya and Tanzania, which killed more than 200 people, and the 2002 attacks on Israeli targets in Kenya.
The US has offered a reward of $5m for information leading to the capture of Mr Mohammed.
"The best way to get America's support to the Somali people in a way that doesn't undermine our interests and their interests is for them to give up these foreign terrorists," Ms Frazer said, after meeting Somalia's President Abdullahi Yusuf in Kenya.
Pressure for peace
Mr Yusuf then left for the Sudanese capital, Khartoum, for talks with a delegation from the Union of Islamic Courts.
But he said he would not hold direct talks with the 10-member delegation from the courts, led by deputy chairman Sheikh Husein Mohamud Jumaale.
The two sides have started direct talks after Sudanese President Omar al-Bashir and Arab League secretary-general Amr Moussa spoke to the delegations separately.
BBC East Africa correspondent Karen Allen says accusations by the government that the Islamists are backed by foreign fundamentalists, and counter-claims that the fragile government is getting the support of Ethiopian troops, will make it difficult to find common ground.
But the fact that the talks are happening at all signals progress, our correspondent says.
There are fears of conflict between the Islamic courts, which controls much of southern Somalia, and the interim government, based in Baidoa, 200km north of the capital, Mogadishu.
International pressure is mounting for both sides to negotiate a peaceful settlement and to establish Somalia's first effective national government for 15 years.
The issue of power-sharing and a ceasefire are bound to be on the table, our correspondent says.
The Islamic courts have organised protests in Mogadishu against Mr Yusuf's call for foreign peacekeepers in Somalia.
Both the United Nations and the African Union are sending teams to Somalia to meet the Islamic courts' leaders and assess the possibility of sending peacekeepers, respectively.
Uganda has said it is ready to send troops but only when the security situation improves.