Cox was appointed to the federal bench by President Kennedy in order to appease Senator James Eastland, the powerful chair of the Senate Juciary Committee. Eastland was determined to win an appointment for Cox, his former roommate at Ole Miss, and campaigned shamelessly on his behalf. Eastland reportedly said to Robert Kennedy, "Tell your brother that if he will give me Harold Cox, I will give him the nigger [Thurgood Marshall, who Kennedy was hoping to place on the Second Circuit Court of Appeals]."
Although Cox had assured Robert Kennedy prior to his appointment that he would conscientiously apply federal law, once on the bench he did what he could to frustrate Justice Department initiatives aimed at bringing about integration. Cox was consistently overruled on appeal, but his decisions over delayed suits for many months. In a voter registration case prosecuted in his court by John Doar in March, 1964, Judge Cox referred to a group of black witnesses scheduled to testify as "a bunch of chimpanzees." Cox's remark led Senator Jacob Javits and Congressman Peter Rodino to launch an impeachment drive against Cox. The drive failed, but attracted considerable support and may have served to mellow Cox somewhat.
In February, 1965, Cox threw out the indictments against most Neshoba County conspirators on the ground that all except Rainey and Price were not government officials and therefore could not be charged with acting 'under color of law." The U. S. Supreme Court overruled Cox in 1966 and reinstated the indictments.
When the Mississippi Burning case finally came to trial in October, 1967, the defendants assumed that they had an ally in Cox. He disappointed them by reprimanding the defense at one point saying, "I am not going to allow a farce to be made of this trial." After the jury returned its verdict, Coax declared, "I very heartily endorse the verdict of the jury." He sentenced the defendants to terms ranging from three to ten years. Cox said of his sentences, "They killed one nigger, one Jew, and a white man. I gave them all what I thought they deserved."