The BBC investigation interviewed 27 former terror detainees across Afghanistan who were detained and then released without charge from the Bagram Air Base. All but two claimed abuse.
All but two of the former prisoners, held at Bagram between 2002 and 2008, alleged abuse and neglect. Many claimed they were subjected to beatings, stress positions, over-exposure to heat or cold, loud noise, being forced to remove clothes in front of female soldiers, sleep deprivation and threats with dogs. Four said their lives were threatened at gunpoint during interrogations.
"They did things that you would not do against animals let alone to humans," one former inmate told the network.
Lt Col Mark Wright, a spokesman for the Secretary of Defense Robert Gates, denied the accusations made to the BBC. He insisted that conditions at the military base "meet international standards for care and custody."
Wright told the network that the Pentagon has a policy of treating detainees humanely, but he acknowledged instances in the past when those principles had been violated.
"There have been well-documented instances where that policy was not followed, and service members have been held accountable for their actions in those cases," he told the BBC.
President Obama has banned the use of torture by U.S. military and intelligence personnel. He ordered an investigation into the treatment of terrorism detainees, and a report is due from that probe in July.