France began a murder inquiry in August after Swiss experts found radioactive polonium-210 on his personal effects.
Arafat's medical records say he had a stroke resulting from a blood disorder.
His widow, Suha, objected to a post-mortem at the time, but asked the Palestinian Authority to permit the exhumation "to reveal the truth".
Arafat's body lay in a stone-clad mausoleum inside the Muqataa presidential compound in the West Bank city of Ramallah. The mausoleum was
sealed off earlier this month.
Palestinian officials told the Associated
Press that the remains were taken from the mausoleum to a nearby mosque,
so that Palestinian doctors could take samples from the bones.
With the body removed from the tomb, the scientists will each
take samples and then go to their respective countries to carry out
tests for polonium-210 and possibly other lethal substances. It is believed that the investigation could take several months.
Before the exhumation, the head of the Palestinian committee investigating Arafat's death, Tawfik al-Tirawi, said no journalists would be allowed to observe the exhumation.
"Because [of the] sanctity of the symbol and the sanctity of this event, [the exhumation] should not be permitted to be in front of the media," the former Palestinian intelligence chief said.
A reburial ceremony, with full military honours, is expected to take place later on Tuesday.
Many Palestinians continue to believe Arafat was poisoned by Israel, which saw Arafat as an obstacle to peace and had put him under house arrest. Israel has strongly denied any involvement.
There has also been speculation that he was suffering from HIV or cancer at the time of his death.
Arafat, who led the Palestine Liberation Organisation for 35 years and became the first president of the Palestinian Authority in 1996, fell violently ill in October 2004 inside the Muqataa.
Two weeks later he was flown to a French military hospital in Paris, where he died on 11 November.
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