JOIN USSome of them, mostly Muslims, have spent weeks in jail; others find it impossible to travel freely. Some say they have had their reputations destroyed by the news coverage. Many were questioned or tracked, and say they felt violated and fearful.
Lawsuits filed by suspects since 2006 have pried millions of dollars in settlements from the government. The US Supreme Court this month heard one of the most serious challenges yet, the case of a Kansas man who claims his detention as a "material witness" destroyed his marriage and his career.
Many plaintiffs say they recognise the security challenges the government faces after September 11; but in many cases, they complain, the government refuses to reveal why someone has attracted attention. Without that information, they argue, it is impossible to clear their names.
"It's a runaround," said Ayman Latif, an American who was stranded in Egypt for six months and questioned by US agents last year after his name appeared on a no-fly list. "Maybe they had a hunch about something and my name came up and they were investigating it. But they wouldn't tell me what that hunch was."
The FBI says it needs secrecy to protect sensitive investigations and to avoid giving terrorists clues for avoiding detection.
The government does not disclose how many people it investigates, but an Associated Press analysis gives a glimpse of how the number has grown. Federal terrorism referrals, cases in which investigators have contacted prosecutors for guidanc, have risen 44 per cent since 2002, from 864 to 1,249 in 2010, according to the Transactional Records Access Clearinghouse, a research program at Syracuse University.
At the same time, the number of people on the FBI's consolidated terrorist watch list stands at 450,000, despite efforts since 2006 to winnow it down. Of those, 18,000 have been flagged for extra screening at airports. About 10,000 people are on the no-fly list, 500 to 1,000 of them US citizens.
Some law enforcement experts say agents are simply doing their jobs by investigating leads, some of which pan out and some of which don't.
Moreover, police work is full of instances in which investigators know someone is up to no good, but they don't have enough evidence to make an arrest.