Joseph Osborne, 35, of Jackson, made his initial appearance Monday in Meridian Municipal Court. He's charged with murder in the November 7, 2002, death of Charley Hopkins, 5, of Meridian.
An autopsy revealed the cause of death as suffocation. The child was found dead in his bedroom at the family home on Crabapple Drive.
"Things at the scene led initial investigators to believe it was a natural death," said MPD investigator Darrell Theall.
Investigators say there were several adults in the house at the time and each had to be eliminated as suspects. The attorney general's office got a court order last week to exhume the youngster's remains for further tests.
"They have a little bit more resources than we do, a little bit more contacts," said Theall. "We were pretty much, I wouldn't say at a stopping point, because we felt like we knew where we were heading but we just wanted to tie some loose ends together. And they were able to come in and help us through their resources and get it done."
At the time of Charley Hopkins' death, Osborne was dating the victim's mother. Osborne remains jailed on a $250,000 bond.