Susie Castillo, who was crowned in 2003, representing Massachusetts, says the April 21 pat down left her feeling molested and violated.
The beauty queen accused the female TSA worker of touching her crotch area several times. Castillo said she was in tears after the experience. She took a video shortly after the incident and posted it online.
Castillo was flying home to Los Angeles. She said she turned down the body scanner due to concerns about radiation exposure.
Castillo later complained and was given a TSA comment card. TSA spokesman Luis Casanova says the screener was questioned and did the pat down correctly.
The Associated Press contributed to this story