The most serious of those allegations -- that a Koran had been flushed down a toilet -- was later retracted. But the U.S. military eventually confirmed five cases of what it calls "mishandling" of the Muslim holy book at the facility, including the splashing of a Koran with urine.
The new revelations sparked further anti-U.S. protests across the Muslim world.
Critics say Guantanamo contradicts fundamental ideals of U.S. justice and the rule of law. They say the prison is also damaging America's reputation abroad and should be closed.
On 6 June, former U.S. President Jimmy Carter urged just that. He said such a move would demonstrate Washington's commitment to human rights.
U.S. Senator Joseph Biden, the top Democrat on the Senate Foreign Relations Committee, is calling for an independent commission to investigate Guantanamo. Speaking on ABC's "This Week" on 5 June, Biden said the prison is doing more harm than good.
"I think we should end up shutting it down, [and] moving those prisoners," Biden said. "Those who we have reason to keep, [we should] keep. Those we don't, [we should] let go. But the bottom line is, I think, [that] more Americans are in jeopardy as a consequence of the perception that exists worldwide with its existence than if there were no [Guantanamo facility]."
In an editorial the same day, "The New York Times" said the best thing Washington can do now is to close Guantanamo. It called the prison "un-American," a "national shame," and a "highly effective recruiting tool for Islamic radicals."
Two of the world's top rights organizations -- Human Rights Watch and Amnesty International -- say strong evidence exists that detainees have suffered inhumane treatment and even torture at Guantanamo.
In its latest report on 25 May, Amnesty compared Guantanamo to a modern gulag. Amnesty's executive director, William Schulz, said on 5 June that the reference is "not an exact or a literal analogy." But he did accuse the United States of maintaining what he called an "archipelago of prisons around the world," many of them secret.
Amnesty said the issue goes beyond whether Guantanamo is open or closed.
"Amnesty International has been calling for the last year for the U.S. administration to set up an independent investigation into allegations of torture and ill treatment in Guantanamo Bay and other detention centers that the U.S. is operating around the world," said Josefina Salomon, a spokeswoman for Amnesty International. "And we think this is the key of the issue. If Guantanamo is not brought in line with international human rights standards, it has to be closed."
The United States government, however, is strongly defending the necessity of the prison and its treatment of prisoners there.
President George W. Bush dismissed Amnesty's accusations as "absurd."
"The detainees -- we've had thousands of people detained. We've investigated every single complaint against the detainees," Bush said. "It seemed like to me [Amnesty International] based some of their decisions on the word of -- and the allegations by -- people who were held in detention, people who hate America, people that have been trained, in some instances, to dissemble -- that means not tell the truth -- and so it is an absurd report. It just is."
U.S. Vice President Dick Cheney and Defense Secretary Donald Rumsfeld have also stood behind the treatment of prisoners at Guantanamo. The chairman of the U.S. Joint Chiefs of Staff, General Richard Myers, said the media should focus instead on the vicious acts of the extremists.
On 6 June, Pentagon spokesman Bryan Whitman said Guantanamo serves a "vital purpose" and that there are no plans to shut it down. He said many of the prisoners are "very, very, very dangerous people" who, if released, would return to committing terrorist acts.