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In 1966, New Orleans District Attorney Jim Garrison began an investigation into the assassination. Garrison's investigation led him to conclude that a group of right-wing extremists were involved with elements of the Central Intelligence Agency (CIA) in a conspiracy to kill Kennedy. Garrison concluded that businessman Clay Shaw, head of the International Trade Mart in New Orleans, was part of the conspiracy. On March 1, 1967, Garrison arrested and charged Shaw with conspiring to assassinate President Kennedy. In the course of that investigation, evidence came to light suggesting that Shaw was linked to the CIA through his involvement in the Centro Mondiale Commerciale, a subsidiary of the trade organization Permindex in which Shaw was a board member. The CMC was said to be a front organization developed by the CIA for transferring funds to Italy for "illegal political-espionage activities." An Italian newspaper Paese Sera reported that the CMC had attempted to depose French President Charles de Gaulle in the early 1960s, and made other allegations about individuals it said were connected to Permindex. It was Paese Sera's allegations connecting Shaw to the CIA were what led to Garrison to implicate the CIA in a conspiracy to assassinate Kennedy.
On January 29, 1969, Clay Shaw was brought to trial on charges of being part of a conspiracy to assassinate Kennedy, and the jury found him not guilty. But despite the jury verdict, Garrison maintained the belief that anti-Communist and anti-Castro extremists in the CIA plotted the assassination of Kennedy to maintain tension with the Soviet Union and Cuba, and to prevent a United States withdrawal from Vietnam. In the book JFK and the Unspeakable, author James Douglass alleged that the CIA, acting upon the orders of conspirators with the "military industrial complex", killed Kennedy and in the process set up Lee Harvey Oswald as a patsy. Douglass stated that Kennedy was killed because he was turning away from the Cold War and pursuing paths of nuclear disarmament, rapprochement with Fidel Castro, and withdrawal from the war in Vietnam.
In 1977, the FBI released 40,000 files pertaining to the assassination of Kennedy, including an April 3, 1967 memorandum from Deputy Director Cartha DeLoach to Associate Director Clyde Tolson concerning CIA plots to kill Fidel Castro. According to DeLoach, an aide to President Lyndon Johnson named Marvin Watson "stated that the President had told him, in an off moment, that he was now convinced there was a plot in connection with the assassination. Watson stated the President felt that the CIA had had something to do with this plot."
Gaeton Fonzi was hired as a researcher in 1975 by the Church Committee and by the House of Representatives Select Committee on Assassinations (HSCA) in 1977. At the HSCA, Fonzi focused on the anti-Castro Cuban exile groups, and the links that these groups had with the CIA and the Mafia. Fonzi obtained testimony from Cuban exile Antonio Veciana that Veciana had witnessed his CIA contact conferring with Lee Harvey Oswald. Independent journalist Anthony Summers spoke with a man named Oscar Contreras, a law student at National University in Mexico City, who said that someone calling himself Lee Harvey Oswald struck up a conversation with him inside a university cafeteria, in the fall of 1963. Contreras described "Oswald" as "over thirty, light-haired and fairly short" — a description that did not fit the real Oswald. Fonzi thought it improbable that the real Oswald would at random start a conversation regarding his difficulties in obtaining a Cuban visa with Contreras, a man who belonged to a pro-Castro student group and had contacts in the Cuban embassy in Mexico City.
Fonzi theorized that there was an Oswald impersonator in Mexico City, directed by the CIA, during the period that the Warren Commission concluded that Oswald himself had visited the city. Fonzi's belief was strengthened by statements from other witnesses. On September 27, 1963, and again a week later, a man identifying himself as Oswald visited the Cuban embassy in Mexico City. Consular Eusebio Azcue told Anthony Summers that the real Oswald "in no way resembled" the "Oswald" to whom he had spoken to at length. Embassy employee Sylvia Duran also told Summers that the real Oswald she eventually saw on film "is not like the man I saw here in Mexico City." On October 1, the CIA recorded two tapped telephone calls to the Soviet embassy by a man identified as Oswald. The CIA transcriber noted that "Oswald" spoke in "broken Russian", while the real Oswald was fluent in Russian. On October 10, 1963, the CIA issued a teletype to the FBI, the State Department and the Navy, regarding Oswald's visits to Mexico City. The teletype was accompanied by a photo of a man identified as Oswald who in fact looked nothing like him.
On November 23, 1963, the day after the assassination of President Kennedy, FBI Director J. Edgar Hoover's stated in a memo:
The Central Intelligence Agency advised that on October 1st, 1963, an extremely sensitive source had reported that an individual identifying himself as Lee Oswald contacted the Soviet Embassy in Mexico City inquiring as to any messages. Special agents of this Bureau, who have conversed with Oswald in Dallas, Texas, have observed photographs of the individual referred to above and have listened to a recording of his voice. These special agents are of the opinion that the referred-to individual was not Lee Harvey Oswald."JOHNSON: "Have you established any more about the [Oswald] visit to the Soviet Embassy in Mexico in September?"
HOOVER: "No, there's one angle that's very confusing for this reason. We have up here the tape and the photograph of the man at the Soviet Embassy, using Oswald's name. That picture and the tape do not correspond to this man's voice, nor to his appearance. In other words, it appears that there was a second person who was at the Soviet Embassy."
Fonzi concluded it was unlikely that the CIA would legitimately not be able to produce a single photograph of the real Oswald as part of the documentation of his trip to Mexico City, given that Oswald had made five separate visits to the Soviet and Cuban embassies according to the Warren Commission, locations where the CIA maintained surveillance cameras.
Three men were photographed by several Dallas-area newspapers under police escort near the Texas School Book Depository shortly after the assassination of President Kennedy. These men became known as the "three tramps". They were detained and questioned briefly by the Dallas police. E. Howard Hunt is alleged by some to be the oldest of the tramps. Hunt was a CIA station chief in Mexico City and was involved in the Bay of Pigs Invasion. He later worked as one of President Richard Nixon's White House Plumbers. Others believe that one of the tramps is Chauncey Holt, who claimed to have been a double agent for the CIA and the Mafia, and claimed that his assignment in Dallas was to provide fake Secret Service credentials to people in the vicinity. Dallas police officer Joe Smith and Army veteran Gordon Arnold have claimed to have met a man on or near the grassy knoll who showed them credentials identifying him as a Secret Service agent.
Frank Sturgis is thought to be the tall tramp. Sturgis was also involved both in the Bay of Pigs invasion and in the Watergate burglary. Marita Lorenz, with whom Sturgis had a relationship. Lorenz claimed that Sturgis told her that he had participated in a JFK assassination plot., an allegation that Sturgis later denied. In an interview with Steve Dunleavy of the New York Post, Sturgis said that he believed communist agents had pressured Lorenz into making the accusations against him.
The House Select Committee on Assassinations had forensic anthropologists study the photographic evidence. The committee claimed that its analysis ruled out E. Howard Hunt, Frank Sturgis, Dan Carswell, Fred Lee Chapman, and other suspects. Records released by the Dallas Police Department in 1989 identified the three men as Gus Abrams, Harold Doyle, and John Gedney. In 1975, Hunt testified before the United States President's Commission on CIA activities within the United States that he was in Washington, D.C. on the day of the assassination. This testimony was confirmed by Hunt's family and a home employee of the Hunts.
In August 2003, while in failing health, Hunt allegedly confessed to his son of his knowledge of a conspiracy in the JFK assassination. However, Hunt's health improved and he went on to live four more years. Shortly before Hunt's death in 2007, he authored an autobiography which implicated Lyndon B. Johnson in the assassination, suggesting that Johnson had orchestrated the killing with the help of CIA agents who had been angered by Kennedy's actions as president. After Hunt's death, his sons, Saint John Hunt and David Hunt, stated that their father had recorded several claims about himself and others being involved in a conspiracy to assassinate President John F. Kennedy. In the April 5, 2007 issue of Rolling Stone, Saint John Hunt alleged that his father had implicated a number of individuals in the assassination, including Lyndon Johnson, Cord Meyer, David Phillips, Frank Sturgis, David Morales, Antonio Veciana, William Harvey, and Lucien Sarti.
Fonzi and others believe that CIA operative David Morales was involved in the Kennedy assassination. Morales' friend, Ruben Carbajal, claimed that in 1973 Morales stated that "Kennedy had been responsible for him having to watch all the men he recruited and trained get wiped out. Well, we took care of that SOB, didn't we?" Morales had openly expressed deep anger toward the Kennedys for what he saw as their betrayal during the Bay of Pigs Invasion.
Many conspiracy theorists have argued that Oswald's pro-Communist behavior may have been a carefully planned ruse by U.S. intelligence agencies to infiltrate left-wing organizations in the United States and to conduct counterintelligence operations. Oswald himself claimed to be innocent, denying all charges and even declaring to reporters that he was "just a patsy". He also insisted that the photos of him with a rifle had been faked, an assertion contradicted by statements made by his wife, Marina (who claimed to have taken the photos), and the analysis of FBI photographic experts. Some FBI employees had made statements indicating that Oswald was indeed a paid informant, but FBI agent James P. Hosty reported that his office's interactions with Oswald were limited to dealing with Oswald's complaints about being harassed by the Bureau for being a communist sympathizer. In the weeks before the assassination Oswald made a personal visit to the FBI's Dallas branch office with a hand-delivered letter, but, Hosty destroyed the letter by order of J. Gordon Shanklin, his supervisor.
Some researchers have alleged that Oswald was an active agent of the Central Intelligence Agency, noting his attempt to defect to Russia, and subsequently being able to return without difficulty. Oswald was even able to receive a repatriation loan from the State Department. A former roommate of Oswald, James Botelho (who would later become a California judge) stated in an interview with Mark Lane that he believed that Oswald was involved in an intelligence assignment in Russia. Oswald's mother, Marguerite, often insisted that her son was recruited by an agency of the U.S. Government and sent to Russia. Jim Garrison also held the opinion that Oswald was most likely a CIA agent who had been drawn into the plot to be used as a scapegoat. Senator Richard Schweiker, a member of the U.S. Senate Select Committee on Intelligence said of Oswald that "everywhere you look with him, there're fingerprints of intelligence". In 1978, former CIA paymaster and accountant James Wilcott testified before the HSCA, stating that Lee Harvey Oswald was a "known agent" of the Central Intelligence Agency.
Some conspiracy theorists have alleged a plot involving elements of the Mafia, the CIA and the anti-Castro Cubans, including Anthony Summers, who relies on government documents which show that, beginning in 1960, these groups had worked together in assassination attempts against Cuban leader Fidel Castro. Author Ruben Castaneda concluded: "Based on the evidence, it is likely that JFK was killed by a coalition of anti-Castro Cubans, the Mob, and elements of the CIA." In his book, They Killed Our President, former Minnesota governor Jesse Ventura also concluded: "John F. Kennedy was murdered by a conspiracy involving disgruntled CIA agents, anti-Castro Cubans, and members of the Mafia, all of whom were extremely angry at what they viewed as Kennedy's appeasement policies toward Communist Cuba and the Soviet Union."