The wife of one of the three detainees told The Associated Press before the flight arrived today that she was waiting for her husband, detainee Boudella al Hajjare.
Police were seen rushing men out of the building, putting them in armoured vehicles and taking them to state police headquarters.
A U.S. federal judge ruled last month they should be released, saying the U.S. government's evidence linking the men to al Qaeda was not credible because it came from a single, unidentified source.
It is the first release from Guantanamo ordered by a U.S. federal judge.
Mustafa Ait Idr, one of the released prisoners, told a private television station upon arriving in Bosnia that interrogators broke one of his fingers and that his captors desecrated the Quran, Islam's holy book.
The 38-year-old Algerian and two other Algerian-born naturalized Bosnians were detained in 2001 on suspicion of plotting to bomb the U.S. Embassy in Sarajevo.
They had been held at Guantanamo since January 2002.
Pentagon spokesman Navy Cmdr. Jeffrey Gordon denied the accusations of abuse.
"The Department of Defense policy is clear," Gordon said. "We treat all detainees humanely."
He said that 12 major reviews conducted of detention operations in recent years did not find any policy that condoned abuse.
The cases of more than 200 additional Guantanamo detainees are still pending, many in front of other judges in Washington's federal courts.
Saudi Prisoner On Hunger Strike For Three Years
A judge has ordered an independent medical exam for a Saudi prisoner at Guantanamo who has been on hunger strike for more than three years.
U.S. District Judge Emmet Sullivan ruled Thursday after a hearing in Washington that a court-appointed medical expert will evaluate the physical and mental health of Ahmed Zuhair, whose lawyers say has deteriorated sharply in recent weeks.
Sullivan also ordered the release of Zuhair's medical records.
The judge denied a defense request to halt the use of restraints when the prisoner is force-fed at Guantanamo. He also refused to order the U.S. to stop using a corn-based liquid nutrient to feed the prisoner that his legal team says may be causing an allergic reaction.
Last month, his lawyer returned from visiting Zuhair and said his client appeared to weigh no more than 100 pounds and was vomiting repeatedly during meetings at the American base in Cuba.
U.S. authorities have said Zuhair is in no danger and has been combative with guards.
Zuhair has been on a hunger strike to protest his confinement since the summer of 2005. He has not been charged with a crime, but the U.S. says he trained with the Taliban and al Qaeda in Afghanistan and was a member of an Islamic fighting group in Bosnia in the mid-1990s.
War Crimes Charges Filed Against Two Prisoners
A spokesman for the Office of Military Commissions says prosecutors have filed war-crimes charges against two Guantanamo detainees, accusing them of training al Qaeda recruits in Afghanistan.
Joseph DellaVedova says the maximum sentence both men could receive is life in prison.
DellaVedova says Sudanese prisoner Noor Uthman Muhammed is accused of conspiring with al Qaeda and providing support for terrorism. Muhammed was allegedly a weapons instructor from 1996 and 2002.
Tariq Mahmoud Ahmed al-Sawah, an alleged explosives trainer, is charged with providing support for terrorism and conspiring against U.S. and coalition forces.
The charges must be approved by a Pentagon legal official.