The three, ranging from 13 to 15 years old, were the only juveniles among 660 suspected Taliban and al-Qaida fighters being held without charge at the US naval base.
Detention of the prisoners, especially the youngsters, has drawn major criticism from human rights groups and governments who have urged the United States to file charges against the detainees or release them.
The Pentagon did not say where the three juveniles were flown, but one US official told Reuters the youngsters were returned to Afghanistan - where they were arrested more than a year ago - to be set free.
"With the assistance of non-governmental organisations, the juveniles will be resettled in their home country. It is our goal to return them to an environment where they have an opportunity to re-integrate into civil society," the defence department said in a statement.
It said that senior US officials had decided to free the three because they were no longer a threat to America in the terror war sparked by September 2001 attacks on America.
Most of the prisoners at Guantanamo were captured in the war in Afghanistan following the attacks that Washington blames on fugitive Usama bin Ladin's al-Qaida network.
Age 'not a determining factor'
The release of the three juveniles brought to 91 the number of detainees removed from the US Navy Base prison since the expanded facility was built there after the attacks.
Four of those were returned to Saudi Arabia for continued detention and the others to their home countries to be set free.
"Age is not a determining factor in detention. We detain enemy combatants who engaged in armed conflict against our forces or provided support to those fighting against us"
"Senior leadership, in consultation with other senior US government officials, determined that the juvenile detainees no longer posed a threat to our nation, that they have no further intelligence value and are not going to be tried by the US government for any crimes," the Pentagon said.
"Age is not a determining factor in detention. We detain enemy combatants who engaged in armed conflict against our forces or provided support to those fighting against us."
Captured during raids
Two of the three were captured during raids by US and allied forces on Taliban camps and a third was arrested while trying to obtain weapons to fight American troops, the announcement said.
Although none of the prisoners has been charged, US defense officials have said that some could soon be charged and tried by military commissions authorised by President George Bush.
Protests have been held globally
for release of detainees
In the face of criticism of the prisoner policy, a senior Pentagon official in the past described the juveniles as enemy combatants who despite their age were "very, very dangerous people" who "have stated they have killed and will kill again."
The Defence Department said on Thursday that after medical tests determined that all three were under the age of 16, the juveniles had been housed in a separate detention facility "modified to meet the special needs of juveniles" and were given access to the International Red Cross.
"In this facility, they were not restricted in the same manner as adult detainees and underwent assessments from medical, behavioural, educational, intelligence and detention specialists to address their unique needs," it said.