All five suspects could face the death penalty if convicted.
They were transferred to Guantanamo in Cuba in September 2006 after spending about three years in secret CIA prisons.
Thursday's arraignment poses the highest-profile test yet of a US military tribunal system that faces an uncertain future.
The US supreme court struck down an earlier system as unconstitutional in 2006, and is to rule this month on the rights of Guantanamo prisoners, potentially delaying or halting the proceedings.
With less than eight months remaining in office for George Bush, the US president, presidential candidates Barack Obama and John McCain both say they want to close the military's offshore detention centre.