Khalid al-Fawwaz is accused on four counts of conspiracy to kill Americans and conspiracy to destroy US property, and faces life behind bars if convicted.
The attacks on the US embassies in Kenya and Tanzania killed 224 people and wounded around 5,000 others.
Arrested in Britain in 1999, when he was allegedly head of the British cell of Al-Qaeda, he has already spent 16 years in custody and pleads not guilty.
Fawwaz on Tuesday took a seat in the Manhattan court room, just a short walk from the site of the former Twin Towers destroyed by Al-Qaeda in the 9/11 attacks.
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He had dark shadows under his eyes, his face was pale and partially obscured by a long, pointy grey beard.
He folded his stocky frame into a court chair, put black-rimmed spectacles on his nose to consult documents and exchanged pleasantries with his lawyers.
US District Judge Lewis Kaplan, who has overseen a string of terror trials ending in guilty convictions, opened the first stage of jury selection on Tuesday.
A pool of around 200 prospective jurors, who have already completed questionnaires, will be whittled down to 12, with six alternates, who will hear the case.
The Fawwaz trial is estimated to last five weeks, considerably shorter than previously expected.
One of his co-defendants, Libya's Abu Anas al-Libi, died in a New York hospital earlier this month after suffering from advanced hepatitis C and cancer.
A second Egyptian, Adel Abdel Bary, pleaded guilty last year and is set to be sentenced by Kaplan on February 6.
Fawwaz was arrested in Britain in 1999 and fought a nearly 12-year battle against extradition before being sent to the United States to stand trial.