Munir Al-Mutassadiq, 30, is accused of conspiring with an al- Qaida cell in Hamburg to stage the aircraft hijackings in which nearly 3000 people died.
He was charged on Tuesday with plotting the attacks alongside Muhammad Ata and others, and with membership of a terrorist organisation.
Presiding judge Ernst-Rainer Schudt promised the accused a fair trial independent of the wishes of government and of public expectations and one that would provide a definitive answer as to his involvement.
"The black hole in the chain of evidence will close. We will certainly not sink into it," he said.
In February 2003, al-Mutassadiq became the first person anywhere to be convicted in connection with the 9/11 attacks and was sentenced to 15 years in jail.
But in March this year, a higher court ruled the verdict was unsatisfactory because judges had not had access to testimony from Ramzi bin al-Shaiba, a key member of the al-Qaida Hamburg cell who was captured in Pakistan in 2002. It ordered a new trial.
Doubts surround the prospects for the new proceedings because the US has so far refused, on security grounds, to allow bin al-Shaiba and others to be questioned.
On the eve of the retrial, a court spokeswoman in Hamburg said the US had still not responded to a request filed in May to allow testimony from six key witnesses, including bin al-Shaiba, suspected 9/11 plotter Zakaryia Musaui and former CIA chief George Tenet, who resigned earlier this year.