Khalid Sheikh Mohammed and four other men accused of plotting the 9/11 attacks are to be charged by a military tribunal at Guantanamo Bay.
An earlier attempt was halted three years ago when President Barack Obama tried to shut Guantanamo down.
New rules for Guantanamo trials have been since introduced, including a ban on evidence obtained under torture.
However, defence lawyers still say the system lacks legitimacy, because of restricted access to their clients.
President Obama's efforts to hold Khalid Sheikh Mohammed's trial in New York foundered in the face of political and public opposition and it will now be held at a military tribunal in Guantanamo Bay, as previously planned.
A small number of victims' relatives have arrived at the military complex to attend the arraignment.
'Proud' of attacks
Self-proclaimed 9/11 "mastermind" Khalid Sheikh Mohammed and the four others - Waleed bin Attash, Ramzi Binalshibh, Ali Abd al-Aziz Ali and Mustafa Ahmad al-Hawsawi - are expected to be tried together.
They are accused of planning and executing the terror attacks of 11 September 2001, which saw hijacked planes strike New York, Washington and Shanksville, Pennsylvania and left a total of 2,976 people dead.
At Saturday's arraignment, they will be read charges including terrorism, hijacking, conspiracy, murder and destruction of property.
They are expected to be asked to enter a plea for the first time.
Jim Harrington, the civilian lawyer for Ramzi Binalshibh, told Associated Press that although his client had previously said he was "proud" of his role in the attacks he had "no intention of pleading guilty".
"I don't think anyone is going to plead guilty," he added.
The decision to hold a military rather than a civilian trial remains controversial and follows a lengthy legal wrangle over where the five men would face justice.
In 2009 the Obama administration tried to move their trial into US civilian courts, but reversed its decision in April 2011 after widespread opposition.
The five were eventually charged in June 2011 with offences similar to those they were accused of by the Bush administration.
The Pentagon has previously said Khalid Sheikh Mohammed, who is of Pakistani origin but was born in Kuwait, admitted he was responsible "from A to Z" for the 9/11 attacks.
In a previous court hearing he has said that he intended to plead guilty and would welcome martyrdom.
He was captured in Pakistan in March 2003 and has been detained at Guantanamo Bay since 2006.
US prosecutors allege that he was involved with a host of other terrorist activities.
These include the 2002 nightclub bombing in Bali, Indonesia, the 1993 World Trade Center bombing, the murder of American journalist Daniel Pearl and a failed 2001 attempt to blow up an airliner using a shoe bomb.
Khalid Sheikh Mohammed has alleged that he was repeatedly tortured during his detention in Cuba.
CIA documents confirm that he was subjected to simulated drowning, known as waterboarding, 183 times.
Also facing trial are:
- Waleed bin Attash, a Yemeni
- Ramzi Binalshibh, a Yemeni who allegedly helped find flight schools for the hijackers
- Ali Abd al-Aziz Ali, accused of helping nine of the hijackers travel to the US
- Mustafa Ahmad al-Hawsawi, a Saudi, accused of helping set up the hijackers with money, clothes and credit cards