U.S. District Judge Marcia Cooke said that although it would be "naive" to ban all references to the 2001 attacks, the charges in the Miami case do not allege a direct connection between the defendants and the attacks and should not be used to suggest guilt by association.
"Any idea, through inference or otherwise, that these defendants are connected to 9/11 is not available to the government," Cooke said. "If it's not what this case is about, it should not be brought into this case."
Prosecutor John Shipley said there was never any intent to link Padilla and the other defendants to the conspiracy or the attacks, blamed on al Qaeda, that killed about 3,000 people. But he said there will be testimony connecting the defendants to the terror group led by Osama bin Laden.
"They certainly supported al Qaeda, there's no question about that," Shipley said. "We're not going to try them for their specific involvement in 9/11."
After the exchange over Sept. 11 references, the first group of 18 potential jurors was brought in for questioning. Selection for 12 jurors and six alternates is expected to take about two weeks, with the trial likely to last at least four months.
Although there is no direct connection, the shadow of the Sept. 11, 2001, attacks hangs over the case. Dozens of potential jurors mentioned the attacks when they filled out questionnaires meant to gauge their ability to be fair and impartial.
Padilla was held for 3 1/2 years as an enemy combatant in a military brig before being added to the Miami case. He and co-defendants Adham Amin Hassoun and Kifah Wael Jayyousi face charges of conspiracy to "murder, kidnap and maim" people overseas and of providing support to terror groups. All three pleaded not guilty and could faced life in prison if convicted.
The three are charged with being part of a support cell that funneled fighters, money and supplies to Islamic extremists in Afghanistan, Chechnya, Bosnia, Tajikistan and elsewhere around the world.
For the first time Monday, Padilla appeared in court wearing a charcoal-gray suit, white shirt and tie in place of the prison jumpsuit he usually wears. He smiled and waved at relatives sitting in the courtroom.
Courtroom security was especially tight, including a temporary wall erected in the lobby to shield potential jurors and witnesses from the public. Cooke said the jurors names and likenesses could not be made public for the duration of the trial.
The trial's start comes five years after Padilla was arrested in Chicago. In 2002, then-Attorney General John Ashcroft said authorities had thwarted an al Qaeda plot with Padilla to detonate a radioactive "dirty bomb" in a major city. Those allegations have been dropped.
Padilla was hastily added to an existing case in Miami in November 2005, a few days before a Supreme Court deadline for Bush administration briefs on the question of the president's powers to continue holding him in military prison without charge.
Padilla claimed he was tortured while interrogated in military custody — a charge repeatedly denied by the Bush administration — and sought unsuccessfully to have his case dismissed for "outrageous government conduct."
Federal officials claim Padilla admitted involvement and training with al Qaeda during his interrogations in a military prison, as well as the proposed "dirty bomb" plot and another plan to blow up apartment buildings. However, none of that can be used as evidence because Padilla had no lawyer present and was not read his Miranda rights.
"If he's acquitted, it's going to be a cautionary tale about denying full constitutional rights to U.S. citizens who are accused of a crime," said Michael Greenberger, a University of Maryland law professor.
Prosecutors say Hassoun, 45, acted as a South Florida recruiter and fundraiser for violent Muslim causes. Padilla, 36, a one-time street gang member in Chicago, allegedly became a recruit. Padilla had converted to Islam in a Florida prison while serving a year for a 1991 weapons conviction.
A key piece of evidence is a purported "mujahedeen data form" that prosecutors say Padilla completed in 2000 — his fingerprints are supposedly on it — to join an al Qaeda training camp in Afghanistan.
Jayyousi's alleged major role was publication of the "Islam Report," which prosecutors say was used to spread extremist Islamic ideology and assist in fundraising and terror support. Jayyousi, 44, contends he was only reporting on global events of Muslim interest, and his lawyer says prosecutors are attempting to expand the case into a trial of Islamic political and religious groups.
"The trial will ultimately become the United States vs. Islam," said Jayyousi lawyer William Swor.
The alleged conspiracy goes back more than a decade, with prosecutors claiming more than 50,000 intercepted telephone calls and bugged conversations in Arabic with purported code words.
Yet there is little proof that the three were directly responsible for any specific acts of terrorism. In court papers, prosecutors listed generalized victims such as Serbian and Croat forces in the 1990s Bosnian war, the Russian army in Chechnya and "moderate" Muslim governments in Libya, Tunisia and elsewhere.
Defense lawyers say providing assistance to one faction in these conflicts does not necessarily amount to a crime.
"Killing only becomes murder under certain specific circumstances," said Hassoun's lawyer, Jeanne Baker. "Defending Muslims is not committing murder."
Padilla's voice is only heard on eight of the FBI wiretaps and he is mentioned on about 20 others. One of those says he had gone to "the area of Osama," an apparent reference to bin Laden's al Qaeda camps in Afghanistan.