Elizabeth Kushigian spent time in an isolation room at Miami International Airport every time she returned from an international trip – until a senator got her taken off a DHS watchlist. For years, Elizabeth Kushigian never had a problem flying back-and-forth to Costa Rica, where she runs a local micro-lending nonprofit. But in 2004, she suddenly found it impossible to re-enter the United States without being ordered into a special isolation room at Miami International Airport. There, she'd wait for extra scrutiny.

"I was in the line where you come in and stamp your passport, and each time they would scan the passport and look at (the) screen and stiffen," Kushigian says. "I was on some sort of list. I don't know why; it could have been because of something I did in the '60s and in the early 1980s, I did some civil disobedience on behalf of El Salvador."

Kushigian is just a member of a growing club of American citizens whose lives have been touched by a slew of government watch lists proliferating with little oversight or redress mechanisms since the 9/11 attacks. Containing, by some estimates, hundreds of thousands of names submitted by dozens of agencies, the lists have not only snagged people like Kushigian – who wind up on them for mysterious reasons – they've also stigmatized and inconvenienced thousands of others whose names happen to be similar to an entry on the list.

The issue returned to national debate last week after one of the nation's most respected constitutional law professors was told by an airline official that he'd been placed on a watch list for his criticism of the president, a claim that U.S. officials deny.

Kushigian's hassles at the airport ranged from minor delays to full-blown interrogations. The second time she was pulled aside at the border, officials with the Bureau of Immigrations and Customs Enforcement demanded to know how she could afford to travel on her salary. When she explained that she'd inherited money from her father, they peppered her with questions about what his factory used to make, and what charities he donated to.

"It was unnerving sitting in that little room even for a short period of time, Kushigian says. "You get a sense of what people who are not senators and not citizens go through."

Kushigian tried to figure out why she'd been targeted by filing a Freedom of Information Act request, but learned nothing. Then she turned to her elected representatives in Massachusetts, including Sen. Ted Kennedy, who himself was famously fingered by a watch list in 2004. Eventually Kennedy's office sent along a letter signed by the head of Immigration and Customs, which said in part: "With respect to Mrs. Kushigian's specific situation, we are pleased to report that action has been taken in order that she not be subjected to automatic special attention when arriving at U.S. Ports-of-Entry."

Kushigian was one of the lucky ones: Winning even a tacit acknowledgement that she was on a list is a rare victory over the federal homeland security bureaucracy. Tens of thousands of travelers have applied to get help from the Transportation Security Administration, which now has three lists: a no-fly list of persons considered too dangerous to be allowed on a plane or cruise ship; a selectee list of people who must undergo extra screening to fly; and a white list of persons who have names similar to those on the other lists, but who are not threats.

The last publicly reported tally of the no-fly and selectee lists in October 2006 put the combined number of names at 119,000. The current number is a closely guarded secret, but Homeland Security officials announced earlier this year that it cut the no-fly list in half after hand-reviewing the names, which are submitted by a hodgepodge of U.S. intelligence agencies.

Despite that, last month constitutional scholar Walter F. Murphy, McCormick Professor of Jurisprudence Emeritus at Princeton University, found himself unable to check in curbside at a New Mexico airport. A check-in clerk with American Airlines told him it was because he was on a "terrorist watch list," Murphy says.

"One of them, I don't remember which one, asked me, 'Have you been in any peace marches? We ban a lot of people from flying for that,'" recalls Murphy. "I said, 'No, but I did give a speech criticizing George Bush,' and he said, 'That will do it.'"

Incensed at the thought that the administration was using an anti-terrorism measure for political purposes, Murphy publicized his run-in through a prominent law blog, Balkinization. His accusations lit up the comment boards on several influential websites.

The evidence remains thin that Murphy was actually on a watch list – he was able to get a boarding pass on his return trip – but the incident shows how the watch list programs have put their imprint on America's consciousness. It's in the very nature of secret watch lists to induce paranoia, says Lee Tien, an Electronic Frontier Foundation lawyer and longtime critic of government watch lists.

"If (the lists) weren't secret, you would know if you were on one and you would be able to scream about it," Tien says. "Without accountability, they will be stupid or evil; and without transparency, there's no way to tell the difference."

Following a string of high profile cases of watch lists snaring innocent travelers – ranging from U.S. armed forces personnel, to prominent politicians and nuns – the Department of Homeland Security launched a website in February to help out people who are wrongly matched with names on the list. Travelers can fill out a complaint form online, and so far, 3,700 people have applied for help.

That's a big change for the government, which didn't even admit that it had a no-fly list until fall of 2002. The existence of a second list, known as the "selectee list", was also kept secret until it surfaced in documents obtained under the Freedom of Information Act by the Electronic Privacy Information Center, and first reported by Wired News.

Those lists also largely derived from the "unified terrorist watch list," a blend of information from intelligence agencies and the FBI that's also shared with the FBI's National Crime Information Center. The NCIC database is queried nearly any time a cop or county sheriff makes an arrest or pulls someone over for speeding.

The Treasury Department runs a separate list known as the OFAC list (short for Office of Foreign Assets Control), which is the only published government anti-terrorism watch list. The 250-page long list includes organizations and individuals with which American companies are prohibited from doing business.

While there are almost no American citizens on the OFAC list, it is routinely used during home purchases, credit checks and even apartment rentals, and has caused people with common Latino and Muslim names to be denied mortgages for having a name that only vaguely resembles a name on the list, according to a recent report (.pdf) from the Lawyers' Committee for Civil Rights.

The transparency of the public OFAC list is a double-edged sword: Unlike the other watch lists, people can easily determine if a name similar to theirs is on the OFAC list. At the same time, because it's unclassified and published, the OFAC is widely used by companies that run background checks. The potential for of civil liberties abuse is high, says Shirin Shinnar, who wrote the LCCR report.

"If you are denied an apartment or a job, you often aren't told at all why – let alone that it was because you were identified as a possible terrorist," Shinnar says.

Just as murky is the question of how useful the lists actually are. The Transportation Security Administration refuses to provide any statistics on whether the lists have ever prevented any known terrorist from boarding a plane.

For its part, the Terrorist Screening Center, which compiles the unified terrorist watch list created by a 2003 presidential directive, did not respond with a request for comment. But a 2005 Inspector General report (.pdf) found the center's database of hundreds of thousand of records was plagued with technical difficulties and inaccurate entries.

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