President Bush's refusal to apply the Geneva Conventions to those captured during the international armed conflict in Afghanistan and transferred to the US naval base at Guantànamo Bay, Cuba, was challenged by a judicial decision in November. The ruling resulted in the suspension of trials by military commission in Guantànamo, and the government immediately lodged an appeal. The US administration's treatment of detainees in the "war on terror" continued to display a marked ambivalence to the opinion of expert bodies such as the International Committee of the Red Cross and even of its own highest judicial body. Six months after the Supreme Court ruled that the federal courts had jurisdiction over the Guantànamo detainees, none had appeared in court. Detainees reportedly considered of high intelligence value remained in secret detention in undisclosed locations. In some cases their situation amounted to "disappearance".

The "war on terror" and the "war on drugs" increasingly merged, and dominated US relations with Latin America and the Caribbean. Following the US elections in November, the Bush administration encouraged governments in the region to give a greater role to the military in public order and internal security operations. The blurring of military and police roles resulted in governments such as those in Brazil, Guatemala, Honduras, Mexico and Paraguay deploying military forces to deal with crime and social unrest.