Many of the positions ER championed were controversial, especially in the areas of civil rights, civil liberties, housing, women's rights, human rights, and the United Nations. FBI Director J. Edgar Hoover disagreed with ER's stances, had little respect for her, and instructed his agents to keep a close watch on ER. The more she spoke out against Jim Crow laws, opposed the investigative techniques used by the House Committee on Un-American Activities, and supported the United Nations, the more dangerous Hoover thought her conduct. He thought ER's strong defense of civil liberties and civil rights during World War II and the early Cold War proved that she was either a communist or a pawn of the communists, and instructed the FBI to monitor her activities and tape her telephone conversations. Agents, eager to please Hoover, assembled reports, rumors, editorials, gossip, allegations, and aspersions for Hoover's review. The result is one of the largest FBI files in American history, almost ninety percent of which relates to ER's position on civil rights.

Read Eleanor Roosevelt's FBI File (FBI Freedom of Information Act website)
 

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Sources:

Black, Allida. Casting Her Own Shadow: Eleanor Roosevelt and the Shaping of Postwar Liberalism. New York: Columbia University Press, 1996, 151-176.