The 55-year-old star, his wife, and their baby Carmen had been vacationing in the Bahamas. Baldwin says the pat-down happened Monday as they boarded their flight home.
Baldwin tweeted, "Flying from Nassau, Bahamas 2 NY. TSA "random selects" my 5 month old daughter 4 a pat down. I am not kidding. #travelinginUSisadisgrace"
The TSA responded saying that it's required to screen everyone, regardless of age.
KGO-TV San Francisco, CA contributed to this report.