Israeli police have stormed the Temple Mount in Jerusalem and fired tear gas after Palestinian youths reportedly threw stones after Friday prayers.
Several arrests were made during the clash
Many worshippers took refuge in the al-Aqsa mosque - one of Islam's holiest sites - but some young men in the doorway threw stones at the police.
After several hours a deal was reached to allow people to leave peacefully.
The compound - known to Arabs as the Noble Sanctuary - has seen many clashes between Israelis and Palestinians.
The Temple Mount was the scene of a controversial visit by Ariel Sharon - then Israeli opposition leader - in September 2000.
The visit helped spark the latest Palestinian uprising, or intifada.
The BBC's James Reynolds in Jerusalem says Israel often bans worshippers under the age of 40 from attending Friday prayers at the mosque.
But this time, the police say there were no restrictions.
The Israeli police stormed the square using tear gas, rubber bullets, and stun grenades to disperse the crowd following reports of stone-throwing by young Palestinians.
An Israeli police spokesman told AFP news agency that action had been taken only after Palestinian youths had pelted Jewish worshippers praying nearby.
However a member of the Islamic board which oversees the compound said the police raid had been unprovoked.
At least six people were reported to have been wounded.
After several hours, the Israeli police and Muslim religious authorities agreed a deal and those inside the mosque were allowed to leave peacefully.
Earlier, Mr Sharon gave a thinly-veiled warning that Palestinian leader Yasser Arafat could be targeted for assassination.
The Israeli prime minister told Israeli newspapers that both Mr Arafat and the leader of Lebanese militant group Hezbollah should not "feel immune".
"Anyone who kills a Jew or harms an Israeli citizen, or sends people to kill Jews, is a marked man," he said.
Mr Sharon made the remarks in a series of interviews published on Thursday and Friday to mark the Jewish Passover holiday.
"Arafat has no insurance policy... everyone already knows that Arafat is an obstacle to any progress," he told Israel's Maariv newspaper
Last year Israel's security cabinet decided in principle to "remove" Mr Arafat.
The decision prompted international criticism, and Mr Sharon later said he had no plans to kill Mr Arafat.
Last month Israel assassinated Hamas leader Sheikh Ahmed Yassin in a helicopter strike in Gaza.