FBI Director J. 'Edna' Hoover kept files on hundreds of thousands of LGBTs

Supposedly, the reason Hoover's FBI never went after — or even acknowledged the existence of — organized crime is that one syndicate had compromising photos of the Director and his right hand man, Clyde Tolson (the sole beneficiary of Hoover's will.)
     But that didn't keep the FBI from assembling nearly 100 square feet of files on suspected or proven "sex deviates."
     From the Amazon.com book notes, via gay literary website (now on hiatus) Band of Thebes:

     At the FBI, the “Sex Deviates” program covered a lot of ground, literally; at its peak, J. Edgar Hoover's notorious “Sex Deviates” file encompassed nearly 99 cubic feet or more than 330,000 pages of information. In 1977–1978 these files were destroyed—and it would seem that four decades of the FBI's dirty secrets went up in smoke. But in a remarkable feat of investigative research, synthesis, and scholarly detective work, Douglas M. Charles manages to fill in the yawning blanks in the bureau's history of systematic (some would say obsessive) interest in the lives of gay and lesbian Americans in the twentieth century. His book, Hoover’s War on Gays, is the first to fully expose the extraordinary invasion of US citizens' privacy perpetrated on a historic scale by an institution tasked with protecting American life.
     For much of the twentieth century, when exposure might mean nothing short of ruin, gay American men and women had much to fear from law enforcement of every kind—but none so much as the FBI, with its inexhaustible federal resources, connections, and its carefully crafted reputation for ethical, by-the-book operations. What Hoover’s War on Gays reveals, rather, is the FBI’s distinctly unethical, off-the-books long-term targeting of gay men and women and their organizations under cover of "official" rationale—such as suspicion of criminal activity or vulnerability to blackmail and influence. The book offers a wide-scale view of this policy and practice, from a notorious child kidnapping and murder of the 1930s (ostensibly by a sexual predator with homosexual tendencies), educating the public about the threat of "deviates," through WWII's security concerns about homosexuals who might be compromised by the enemy, to the Cold War's "Lavender Scare" when any and all gays working for the US government shared the fate of suspected Communist sympathizers. Charles's work also details paradoxical ways in which these incursions conjured counterefforts—like the Mattachine Society; ONE, Inc.; and the Daughters of Bilitis—aimed at protecting and serving the interests of postwar gay culture.
     With its painstaking recovery of a dark chapter in American history and its new insights into seemingly familiar episodes of that story—involving noted journalists, politicians, and celebrities—this thorough and deeply engaging book reveals the perils of authority run amok and stands as a reminder of damage done in the name of decency.

     Below: Uniquely Nasty, a Yahoo! News documentary on persecution of LGBTs by the U.S. government, in which the FBI's reprehensible behavior looms large. In respect of the rumored homosexuality of Hoover himself, who lived with his mother until he was 40 and willed most of his earthly possessions to Clyde Tolson, his constant FBI companion, the agency intimidated anyone who thought (and/or said)  Hoover fit the profile of the people whose lives and careers he was damaging:

     Ironically, Hoover’s zeal for fulfilling Congress’ wishes came amid persistent rumors about his own sexuality. One of the documents Francis uncovered is an internal FBI memo to Hoover detailing a March 1952 investigation into a federal employee who was reported to have made a comment at a Washington, D.C., bakery: “Have you heard that the director is a queer?”

     The remark prompted Hoover to order a full-scale probe of the federal worker, a budget analyst at the National Labor Relations Board (NLRB). The worker was “vigorously interrogated” by FBI agents and warned of his “criminal and civil liability for the making of such statements,” the memo states. The budget analyst “appeared to be badly frightened” by the questioning and promised to never repeat the remark; the bureau’s No. 2 official, Clyde Tolson, recommended only that the analyst’s “activities” be reported to the “proper officials” at the NLRB.
     (“Yes,” scribbled Hoover in concurrence.)

     The rumors about Hoover, a lifelong bachelor, stemmed from his unusually close relationship with Tolson, his longtime deputy. Hoover and Tolson “had lunch every day together, they drove into work every day together, they took vacations together, had dinners together,” said Charles, the Penn State historian. “When Hoover died, he willed most of his estate to Tolson. So it’s all very suggestive.”