Jose Padilla was seized from a U.S. jail in 2002, declared an "enemy combatant" and secretly transported to a military brig in South Carolina. He was imprisoned for nearly four years, the first two of which he was prevented from communicating with his lawyers or family, and subjected to extreme abuse

In March 2005, the ACLU and Human Rights First filed a landmark lawsuit charging former Defense Secretary Donald Rumsfeld and other senior military leaders with direct responsibility for the torture and abuse of detainees. The suit was brought on behalf of nine men subjected to torture and abuse under Rumsfeld's command.

In March 2012 the ACLU filed a petition with the Inter-American Commission on Human Rights (IAHCR) against the U.S. on behalf of three Afghanis and three Iraqis who were tortured while held by the American military at detention centers in Iraq and Afghanistan between 2003 and 2004. They were part of a group of men that in 2005 sued then-Defense Secretary Donald Rumsfeld and three senior military officials in federal court for their torture and abuse. That case was summarily dismissed on immunity grounds before reaching the merits.  

During the Bush administration, the practice of "extraordinary rendition" was used to apprehend and detain foreign nationals suspected of involvement in terrorism. The suspect would be arrested and secretly transferred to prisons run by foreign intelligence agencies in countries know to torture, or to CIA-run "black sites."