The Saudi man could face the death penalty if found guilty.
The military trials were suspended when the US President, Barack Obama attempted to follow through with his election promise to permanently close Guantanamo Bay.
Presenter: Lisa Millar, North America correspondent
Speaker: Richard Kammen, lawyer for Abd al-Rahim al-Nashiri; Matt Waxman, associate professor at Columbia University; Eugene Fidell, visiting lecturer at Yale University
MILLAR: Abd al-Rahim al-Nashiri walked into the court room wearing a white prison uniform and black sneakers.
The handful of media there reported him as being "all swagger", waving to the gallery.
It's the first time he's been seen in public for nine years.
His case is the first under the revamped military tribunal procedures but his lawyer Richard Kammen isn't impressed.
KAMMEN: You know we're all going to be dressed in suits. It's going to look like a court. But it is not a real court. There is nothing about this that is fair, legitimate. This is a court organised to convict. It is a court organised to kill.
MILLAR: Matt Waxman, now a professor at Columbia University, was in charge of detainee affairs during the Bush administration and acknowledges this case is important.
WAXMAN: It's the first really high value detainee, high profile detainee to go through this process and it involves the death penalty. If we get to that stage that's going to raise all kinds of interesting, very, very controversial legal, strategic and diplomatic issues.
MILLAR: The Obama administration's attempts to close Guantanamo and move the cases of Al Qaeda suspects to criminal courts in the US failed.
It insists these new tribunals are more transparent. They're being broadcasting to an army base in Maryland with seating for 100.
But Eugene Fidell, an expert in military law who now teaches at Yale says even that change comes with qualifications.
FIDELL: The draconian rules under which the commissions even now are being regulated call for a 40 second delay in the audio portion. I mean think of how long 40 seconds is. It's an eternity.
This is not what I would call spontaneity. This is not really what I would call transparency. The only way you could call it transparency is if you contrasted it with what the rules were before. It's still preposterous really.
MILLAR: Human rights groups and others critical of the process say the fact Abd-al-Rahim al-Nashiri was water boarded during interrogations also complicates this case and means the military will have to confront its use of torture.
The case is also significant for what's ahead - the trial of September 11 mastermind Khalid Sheik Mohammed. Attempts to have him tried in New York were scuttled. He remains at Guantanamo Bay waiting for his case to begin.