The complaint, filed Friday in U.S. District Court in Massachusetts, accuses the State Department of rejecting some applications from transgender citizens or issuing documents with their sex assigned at birth. The lawsuit also accused the department of holding some passports and other documents submitted by transgender and nonbinary people.

For transgender Americans, passports just became a lot more complicated. President Donald Trump issued an executive order saying there are two sexes, male and female, and rejecting the idea that people can transition to a gender identify different from the one assigned at birth.

The A.C.L.U. filed a lawsuit after the president’s administration stopped issuing passports that reflect the gender identity of transgender and nonbinary people.