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A TSA agent waits for passengers to use the TSA PreCheck lane being implemented by the Transportation Security Administration at Miami International Airport on Oct. 4, 2011, in Miami. Joe Raedle/Getty Images

If you were invited to opt into TSA PreCheck when it launched just because you were a frequent flier, that's one more perk you can say goodbye to.

More than 1 million people have enrolled in the Transportation Security Administration's PreCheck, an expedited screening program that lets travelers whiz through airport security by bypassing certain screening measures. When the program first launched in 2011, many frequent fliers were invited to simply opt into TSA PreCheck through their airlines -- no fees required. These PreCheck users never actually received the TSA's "Known Traveler Number" but were included in PreCheck screenings nonetheless.

Now those frequent fliers will now have to formally enroll in TSA PreCheck -- and pay the $85 fee -- if they want to continue to benefit from the program. "Those who previously 'opted-in' via a frequent-flyer program will notice a reduction in the frequency in which they are chosen for TSA PreCheck," the agency wrote on its blog.

Travelers can apply for PreCheck at one of 330 application centers around the country. Membership is $85 for five years. U.S. Customs and Border Protection also offers three expedited clearance programs, including Global Entry, which also include TSA PreCheck.