Sources say the fetus was five to six months along.
The plane's cleaning crew found the dead fetus hours after American Airlines Flight 1942 passengers left the plane, according to Fox 46 Charlotte.
Early Tuesday, an attendant cleaning one of the jetliner's four bathrooms saw a large amount of toilet paper in the lavatory, CBS News reported, citing an unnamed source.
A statement from LaGuardia Airport said flights at Terminal B may experience delays due to an "out of service aircraft".More news: Kovacic to join Sarri's Chelsea?
American Airlines said it would not impact the rest of their fleet. "We will release determination when investigation is complete".
Officials with the Port Authority of New York & New Jersey, which manages the airport, did not return calls for comment.
A traveler who was scheduled to fly out of LaGuardia to Charlotte at 7:55 a.m. was frustrated that her flight was delayed three times without explanation.