Government officials say the six include Khalid Sheihk Mohammad, the suspected mastermind of the attacks, in which hijackers flew planes into buildings in New York and Washington. Another hijacked plane, flight 93, crashed into the fields of western Pennsylvania.
A total of 169 charges are being brought against the six suspects. But in many ways, the United States and its policies will be on trial as well.
Nearly 3,000 people were killed in the attacks of September 11th. Mark Bingham lost his life aboard United flight 93.
His mother, Alice Hoagland lives in Saratoga.
"I'm delighted that the wheels of justice have ground down to this point," said Alice Hoagland.
The Pentagon is charging six Guantanamo Bay detainees with planning the terrorist attacks and will seek the death penalty.
"These charges allege a long term highly sophisticated organized plan by al-Qaeda to attack the United States of America," said Department of Defense Legal Advisor Brig. Gen. Thomas Hartmann.
One of the suspects is the man the U.S. says was the mastermind behind the attacks, Khalid Sheik Mohammad.
Just last week, the head of the CIA said Mohammad was subjected to a controversial interrogation technique called "waterboarding."
Many call the practice torture.
"It's clear the issues of waterboarding, of torture, of secret prisons are going to be front and center in these cases," said Anthony Romero of ACLU.
Congresswoman Anna Eshoo says she is introducing a bill as early as this week that would outlaw the use of waterboarding by any agent of the United States.
She says this first ever trial under the terrorism era military tribunal system must be able to stand up to its critics.
"It has to be open and fair because the entire world will be tuned in so not only the results of the trail and how it proceeds, but how we conduct ourselves," said Rep. Anna Eshoo (D) Palo Alto.
Alice Hoaglan will be among those watching and hoping for justice.
"They deserve to have a through hearing and they deserve to have their ugly deeds brought before the American public," said Hoaglan.
The Department of Defense says the defendants will get the same rights as U.S. soldiers under the military justice system including the right to remain silent, to call witnesses and to know the evidence against them.
It could be months or longer before these trials begin.
