Secret sex sessions of Mrs Roosevelt.
When her wheelchair-bound husband, President Franklin D Roosevelt, heard the tape he went into a jealous rage and ordered the sergeant to be sent to a combat zone within ten hours, according to the files.
The tape recording was made in 1943 and the sergeant, Joseph Lash, later became Eleanor Roosevelt's biographer.
The FBI files reveal President Roosevelt confronted his wife with the evidence.
"This recording indicated quite clearly that Mrs Roosevelt and Lash engaged in sexual intercourse during their stay in a hotel," reads a memo dated December 31, 1943, and signed by FBI agent George Burton.
The dossier was kept on Sgt Lash because of his socialist sympathies and his close relationship with the First Lady, who intervened on his behalf several times before the alleged affair was revealed.
She had struck up a correspondence with Sgt Lash after meeting him at a committee hearing on un-American activities.
The tape recording of her tryst, which has long been lost, was made by Army officers tailing Sgt Lash. An angry Roosevelt ordered the chief of the Army Air Corps to "have Lash outside the United States and on his way to a combat post within ten hours", the file says.
Roosevelt went to drastic lengths to have the incident covered up.
"The President had ordered that anybody who knew anything about this case should be immediately relieved of his duties and sent to the South Pacific for action against the Japanese until they were killed," Burton wrote.
Sgt Lash eventually won a Pulitzer Prize for his 1972 biography, Eleanor and Franklin. He did not mention the affair.