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US-born doctor Baruch Goldstein, 38, burst into the mosque in the Machpela Cave and fired up to 100 bullets at worshippers, according to state TV reports.
Eyewitnesses said Goldstein sprayed people with his automatic Galil rifle, an Israeli-made copy of the Soviet AK47. The shooting spree lasted at least 10 minutes, witnesses added.
The mosque was packed with up to 800 worshippers for prayers in the Muslim fasting month of Ramadan.
Goldstein, wearing the uniform of an army reservist, was found dead in the mosque after the shooting stopped.
Initially, police believed that Goldstein had shot himself but in a later statement they said he had been beaten to death with iron bars.
PLO leader Yasser Arafat said in a TV interview: 'What has happened today in the mosque is a real tragedy and will make a very negative backfire on the whole peace process.'
Israeli Prime Minister Yitzhak Rabin telephoned Mr Arafat, describing the attack as a "loathsome, criminal act of murder" and pledging to take "every possible measure to bring about calm".
Mr Rabin said Israel would launch an investigation into the killings.
Mosque guard Mohammad Suleiman Abu Saleh said he thought that Goldstein was trying to kill as many people as possible and described how there were bodies and blood everywhere.
There were unconfirmed reports that Goldstein had an accomplice inside the mosque.
The injured were taken to the Aghli Hospital in western Hebron, where thousands gathered for news of relatives and friends who were in the mosque at the time of the attack.
The army is reported to have killed 12 Palestinians as rioting erupted outside the hospital as feelings ran high in the aftermath of the shootings.
Dr Daoud Obeidi, director of the Aghli Hospital, said from the shrapnel wounds suffered by some of the worshippers, it appeared hand grenades were used in the attack.
Three hours after the attack, which happened at around dawn, hospital officials could still not say exactly how many were killed and injured.
The Palestine Liberation Organisation has demanded that Israel disarm all 120,000 Jewish settlers in the occupied territories and that the United Nations act to protect Palestinians.
Between 30 and 54 Palestinians are believed to have died in the gun attack by Baruch Goldstein in Hebron.
An official inquiry later ruled that Goldstein had been working on his own and did not have an accomplice.
Goldstein had lived in Israel for 11 years and was a doctor in the Jewish settlement of Kiryat Arba, just outside Hebron.
As the settlement's main emergency doctor he was involved in treating victims of Arab-Israeli violence.
It is reported that his hatred became so intense that eventually he refused to treat Palestinians.
Goldstein had been a member of the Jewish Defence League, a violent organisation established by Rabbi Meir Kahane.
Some settlers treated Goldstein as a saint, establishing a shrine to him that was forcibly removed by the Israeli Government in 1999.
Goldstein is not the first American behind an attack against Palestinians in Israeli-held areas.
In 1982, Alan Goodman staged a shooting spree outside the holy Al Aqsa mosque in Jerusalem, killing two people.
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