The program is called Quiet Skies and although we're just hearing about it, it's been going on for years.
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The Quiet Skies program specifically targets U.S. Citizens not in the terrorist screening data base or suspected of wrongdoing, according to the TSA.
As first revealed to the Boston Globe, under the program thousands of unsuspecting Americans have been watched by armed undercover air marshals.
The marshals take notes on what certain passengers do, who they talk to, even if they use the bathroom.
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Some of the behaviors they watch closely for include excessive fidgeting or sweating, using a computer, a jump in their Adam's apple, a cold penetrating stare, or if they boarded last.
The TSA tells ABC News they follow individuals who may have suspicious erratic travel patterns and this is not a surveillance program, adding it does not take race or religion into account.
The Air Marshal Association President released this statement to the Globe "The Air Marshal Association believes that missions based on recognized intelligence, or in support of ongoing federal investigations, is the proper criteria for flight scheduling. Currently the Quiet Skies program does not meet the criteria we find acceptable."