Following a three month trial, the six women and five men reached verdicts in relation to two of the men but could not agree on the remaining 49 charges.
Bruce Houlder, QC, prosecuting, told the Old Bailey the crown would be seeking a retrial in relation to the outstanding charges.
The 11 had denied hijack, possessing firearms, possessing explosives, false imprisonment of passengers and false imprisonment of the cabin crew.
The Ariana Boeing 727, carrying 164 passengers and crew, was forced to fly from Afghanistan to the Essex airport in February last year.
A three-day siege followed which ended peacefully with the alleged hijackers surrendering to armed police.
The defendants at the Old Bailey were: Ali Safi, 35, Abdul Shohab, 21, Taimur Shah, 29, Kazim Mohammed, 28, Waheed Lutfi, 23, Reshad Ahmadi, 19, Nazamuddin Mohammidy, 28, Abdul Ghayur, 25, Mohammed Showaib, 26, Aminullah Mohamedi, 42, and Mohammed Safi, 33.
Aminullah Mohamedi was cleared of hijacking and one charge of false imprisonment on the directions of the judge. The jury found him not guilty of the remaining charges.
Waheed Lutfi, 23, was cleared by the jury of hijack but faces retrial on the other charges. Bail was renewed until next Tuesday when the date of the new trial will be fixed.
The defendants, many of them members of an intellectual group, claimed they had been forced to flee Afghanistan because they were due to be executed by the ruling Taliban group.
Lord Thomas QC, defending Mr Mohamedi, told the jury during the trial that the lack of political freedom in Afghanistan would not be tolerated in Britain. He said: "The Taliban are vicious and dangerous nutters."
Mr Mohamedi had told police he was employed by one of the other defendants and did not know anything about the hijack until he got on to the plane.
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Cartoon
Steve Bell on the media's view of the hijack
Useful links
Afghanistan Online
Afghan media
Online centre for Afghan studies
Stansted airport