In 1964, the Warren Commission concluded that there was no persuasive evidence that Oswald was involved in a conspiracy to assassinate the President, and stated their belief that he acted alone. Critics, even before the publication of the official government conclusions, suggested a conspiracy was behind the assassination. Though the public initially accepted the Warren Commission's conclusions, by 1966 the tide had turned as authors such as Mark Lane with his best-selling book Rush to Judgment, and prominent publications such as the New York Review of Books and Life openly disputed the findings of the commission.

In 1979, the House Select Committee on Assassinations (HSCA) agreed with the Warren Commission that Oswald assassinated Kennedy but found its report and the original FBI investigation to be seriously flawed. The HSCA also concluded that at least four shots were fired, that with "high probability" two gunmen fired at the President, and a conspiracy was probable. The HSCA also stated that "the Warren Commission failed to investigate adequately the possibility of a conspiracy to assassinate the President."

Dallas District Attorney Henry Wade told the press that the weapon found in the School Book Depository was a 7.65 Mauser, and this was reported by the news media. But investigators later identified the rifle as a 6.5 Italian Mannlicher Carcano. According to Mark Lane:

 

"The strongest element in the case against Lee Harvey Oswald was the Warren Commission's conclusion that his rifle had been found on the 6th floor of the Book Depository building. Yet Oswald never owned a 7.65 Mauser. When the FBI later reported that Oswald had purchased only a 6.5 Italian Mannlicher-Carcano, the weapon at police headquarters in Dallas miraculously changed its size, its make and its nationality. The Warren Commission concluded that a 6.5 Mannlicher-Carcano, not a 7.65 German Mauser, had been discovered by the Dallas deputies."

 

Some witnesses to the assassination, or to events connected to the assassination, were intimidated or threatened. These include Jean Hill, Richard Carr, Roy Truly, Sandy Speaker, and A. J. Millican. Acquilla Clemmons, who claimed she saw two men at the scene of Officer J.D. Tippit's murder, also claimed she was told to keep quiet about what she saw by a man with a gun who came to her home.

 

Jim Marrs and Ralph Schuster have pointed out what they have characterized as a suspiciously large number of deaths of people connected with the investigation of the assassination. They also point out that there seems to be a pattern of deaths around the times of various government investigations, such as during and just after the Warren Commission investigation, as New Orleans District Attorney Jim Garrison was launching his own investigation, while the Senate Intelligence Committee was looking into assassinations by U.S. intelligence agencies in the 1970s, and when the House Select Committee on Assassinations was gearing up its investigations. Marrs points out that "these deaths certainly would have been convenient for anyone not wishing the truth of the JFK assassination to become public."

Many government records relating to the assassination, including some from the Warren Commission investigation, the House Select Committee on Assassinations investigation and the Church Committee investigation, were kept secret from the public. These secret documents included the president's autopsy records. Some were not scheduled to be released until 2029, however many of these documents were released during the mid to late 1990s by the Assassination Records Review Board due to the President John F. Kennedy Assassination Records Collection Act of 1992. Some of the material released contains redacted sections. Tax return information, which would identify employers and sources of income, has not been released. The existence of large numbers of secret documents related to the assassination, and the long period of secrecy, suggests to some the possibility of a cover-up. One historian noted, "There exists widespread suspicion about the government's disposition of the Kennedy assassination records stemming from the beliefs that Federal officials (1) have not made available all Government assassination records (even to the Warren Commission, Church Committee, House Assassination Committee) and (2) have heavily redacted the records released under FOIA in order to cover up sinister conspiracies." According to the Assassination Records Review Board, "All Warren Commission records, except those records that contain tax return information, are (now) available to the public with only minor redactions."

The Warren Commission findings and the single bullet theory are implausible according to some researchers. Oswald's rifle, through testing performed by the FBI, could be fired by an experienced shooter only three times within five to eight seconds. The Warren Commission, through eyewitnesses, determined that only three bullets were fired as well: one of the three bullets missed the vehicle entirely; one hit Kennedy and passed through Governor John Connally, and the third bullet was the fatal shot to the President. The weight of the bullet fragments taken from Connally and those remaining in his body supposedly totaled more than could have been missing from the bullet found on Connally's stretcher, known as the "magic bullet". However, witness testimony seems to indicate that only tiny fragments, of less total mass than was missing from the bullet, were left in Connally. In addition, the trajectory of the bullet, which hit Kennedy above the right shoulder blade and passed through his neck (according to the autopsy), supposedly would have had to change course to pass through Connally's rib cage and wrist. In the Zapruder film Kennedy appears clearly to move backwards in the last, fatal shot. Unsupported claims have been made that suggest his head jerks forward and then backwards.

Other evidence for the claim of more than three shots fired was the FBI photographs of the limousines, showing a bullet hole in the windshield of the vehicle above the rear-view mirror. The Warren Commission ignored the evidence. The Government's response was that it "occurred prior to Dallas".