[1][2] He was found guilty in state court of three counts of manslaughter on June 21, 2005, the forty-first anniversary of the crime, and sentenced to 60 years in prison.

Killen, along with deputy sheriff of Neshoba County Cecil Price, was found to have assembled a group of armed men who conspired against, pursued, and killed the three civil rights workers.

Samuel Bowers, who served as the Grand Wizard of the local White Knights of the Ku Klux Klan and had ordered the murders to take place,[10] acknowledged that Killen was "the main instigator".

In November 1965 Solicitor General Thurgood Marshall appeared before the Supreme Court to defend the federal government's authority in bringing charges.

Eighteen men, including Killen, were arrested and charged with conspiracy to violate the victims' civil rights[11] in United States v. Price.

The trial, which began in 1966 at the federal courthouse of Meridian before an all-white jury,[12] convicted seven conspirators, including the deputy sheriff, and acquitted eight others.

The student-teacher team found more potential witnesses, created a website, lobbied the United States Congress, and focused national media attention on reopening the case.

In early January 2004, a multiracial group of citizens in Neshoba County formed the Philadelphia Coalition, to seek justice for the 1964 murders.

Led by co-chairs Leroy Clemons and Jim Prince, the group met over several months and then issued a call for justice, first in March 2004 and then on June 21, the 40th anniversary of the murders.

In the fall of 2004, an anonymous donor provided funds through the Mississippi Religious Leadership Council for anyone with information leading to an arrest.

[18] In 2004, Killen said he would attend a petition-drive on his behalf, conducted by the white supremacist Nationalist Movement at the 2004 Mississippi Annual State Fair in Jackson.

[20] Killen's request for a new trial was denied by a circuit court judge and he was transferred to the Central Mississippi Correctional Facility near Pearl.

On March 29, 2006, Killen was moved to a City of Jackson hospital to treat complications of his leg injury sustained in the 2005 logging incident.

[22] On March 23, 2011, District Judge Daniel P. Jordan III adopted Magistrate F. Keith Ball's recommendation to dismiss Killen's lawsuit.

James Hart Stern, a Black preacher from California, shared a prison cell with Killen from August 2010 to November 2011 while serving time for wire fraud.