But the discovery that their son's body and skull had been stuffed with newspaper before burial added a horrific new dimension to their anguish and further fueled their skepticism of the official findings.
"We have been let down again," his father, Kenneth Johnson, told CNN. "When we buried Kendrick, we thought we were burying Kendrick, not half of Kendrick."
Kendrick Johnson was found dead in a gym at Lowndes County High School in January. State medical examiners concluded that the three-sport athlete suffocated after getting stuck in a rolled-up gym mat while reaching for a sneaker.
Death was not accidental, family's autopsy finds
His parents, Kenneth and Jacquelyn Johnson, never have bought that explanation. They won a court order to have their son's body exhumed and a second autopsy performed in June.
New autopsy finds teen death not accident
During an autopsy, internal organs are removed and examined before being returned for burial. But when Dr. Bill Anderson, the private pathologist who conducted the second autopsy, opened up the teen's remains, the brain, heart, lungs, liver and other viscera were missing. Every organ from the pelvis to the skull was gone.
"I'm not sure at this point who did not return the organs to the body," Anderson said. "But I know when we got the body, the organs were not there."
Two entities had custody of Kendrick Johnson's body after his death -- the Georgia Bureau of Investigation, which conducted the first autopsy in January; and the Harrington Funeral Home in Valdosta, which handled the teen's embalming and burial.