Christian Choate's father, Riley Choate of Hammond, Ind., and stepmother, Kim Kubina of Gary, are charged with murder, battery, neglect and criminal confinement, WLS-TV in Chicago reported.
Christian's body was found last week buried under concrete near his grandmother's home, but prosecutors say he was killed April 5, 2009.
On Tuesday, Choate pleaded not guilty to earlier charges of removing a body from a death scene and failing to report it.
The crime was revealed last week after Christian's sister, Christina, told their mother, Aimee Estrada, who called police.
Estrada said she left Choate after he abused her. She said he gained custody of the children and she had not been allowed to see them since 2005.
Police told the Chicago Sun-Times the boy was abused for two to three years, locked in a dog cage naked or chained to a bed frame.
Christina, now 17, told police she was forced to feed and control Christian and punish him for failing to follow orders.
The day before Christian died, police said, he refused to eat and his father beat him.
When he died, Christina said, Kubina made her wrap up the body.