Ms Lindh died of her injuries in hospital on 11 September, a day after the stabbing.
He has identified himself as John Walker in interviews, but his father's last name is Lindh.
Mr Walker Lindh's lawyers had argued that he never had anything to do with terrorist activities.
Lindh, an American, was tried as a civilian and sentenced to 20 years in federal prison.
Lindh is serving a 20-year sentence for aiding the Taliban during the 2001 U.S.-led invasion of Afghanistan.
Would looking for Arab-Americans have turned up a passenger that resembled "American Taliban" fighter John Walker Lindh?
They readily conceded the news value of seeing Walker Lindh's parents and hearing from them for the first time.
But since the murder three years ago of Anna Lindh, the foreign minister, he has had no obvious successor.
In 2003 one of his poems was read at the memorial service of Anna Lindh, the murdered Swedish foreign minister.
On February 19th his foreign minister, Anna Lindh, said that the Social Democrats might decide as early as next year.
"We are proud that our son stood up for his fundamental right of religious freedom, " Lindh's family said in a statement.
The foreign minister, Anna Lindh, the Social Democrats' heir apparent, hugs and kisses the boss of Ericsson, the country's industrial flagship.
John Walker Lindh and David Hicks, fellow travelers of the Taliban, were both captured by American troops in Afghanistan in 2001.
Another who was shot during the uprising and pulled out of the basement along with Lindh was Nasser Nijer Naser al-Mutairi.
Lindh argued that before 2007 Muslim prisoners were allowed to pray together for at least three of Islam's five daily prayers.
CNN: 'American Taliban' wins right to group prayer in prison
The unit Lindh is housed in has 55 cells, and the majority of the prisoners are Muslim, according to court documents.
CNN: 'American Taliban' wins right to group prayer in prison
The judge rejected defence arguments that Mr Walker Lindh was a loyal American, saying "the evidence before the court belies that assumption".
Wednesday's hearing came a day after US authorities formally indicted Mr Walker Lindh on 10 charges, including conspiring to kill fellow Americans.
Lindh joined the prayer lawsuit in 2010, three years after being sent to the prison near the border between Indiana and Illinois.
Lindh, who was born in California, converted to Islam as a teenager.
CNN: 'American Taliban' wins right to group prayer in prison
Mr Walker Lindh, accompanied by federal marshals, was driven by motorcade to the courthouse in Alexandria, Virginia, at 0700 local time (1400 GMT).
During the court hearing, Judge W Curtis Sewell sided with federal prosecutors who maintained that Mr Walker Lindh posed a threat to the public.
As part of a deal, Lindh pleaded guilty to supplying services to the Taliban and carrying an explosive during the commission of a felony.
CNN: 'American Taliban' wins right to group prayer in prison
The suit was originally filed in 2009 by two Muslim inmates in the unit, but it got far more attention when Lindh joined the case.
Still haunted by that killing, Swedes are relieved that Anna Lindh's murderer was caught, and that he has now been sentenced, the BBC's Lars Bevanger in Stockholm says.
"The criminal complaint filed today describes a series of crossroads John Walker Lindh encountered on his way to joining not just one, but two terrorist organizations, " Ashcroft said.
There is no reason why America's own civilian courts, which have successfully tried plenty of domestic and foreign terrorists (including Mr Lindh), could not be adapted to this purpose.
One of the committed jihadis who came out of that basement, wounded and unrepentant, was "American Taliban" John Walker Lindh, now serving a 20-year sentence in a federal prison.
After the hearing, one of his lawyers, James Brosnahan, accused US Attorney General John Ashcroft of using "inappropriate" language and taking out his frustrations about terrorism on Mr Walker Lindh.
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