JoAnn Cunningham, 36, and Andrew Freund Sr., 60, face several counts of murder. Both are accused of killing their son and lying about his disappearance.
SEE INSIDE: Photos from AJ Fruend's home show filthy conditions
A grand jury formally indicted Cunningham on 20 counts, ranging from first degree murder to aggravated battery to a child. She could face life in prison.
Freund was indicted on 41 counts, including murder and aggravated battery of a child. He faces more, but less severe counts than Cunningham. He could also face life in prison.
Freund reported his AJ missing on April 18. After a week-long search for AJ, police confronted his Crystal Lake parents with cell phone evidence and the couple led them to AJ's body, wrapped in plastic and buried in a shallow grave in Woodstock.
WATCH: AJ Freund's body found 6 days after he was reported missing
After looking into the family's history, it was revealed DCFS officials responded multiple times to the home for reports of abuse and neglect. The most recent visit was last December. DCFS came under fire for returning AJ and his brother back into the custody of their parents.
Elva Sedlock and Pamela Spencer helped search for AJ when he was reported missing, they were in court Friday to show their support for the little boy.
"We've been there from the beginning and this is the second court date we showed up to we followed the case to the end and hopefully there is justice for AJ," Sedlock said.
"It's sad, you did it, own up to it," Spencer said.
WATCH: DCFS releases full history with AJ Freund's family
Cunningham and Freund are each being held on a $5 million bond.
Freund's attorney asked the judge to give his client a psychological exam, not to determine if he is fit to stand trial, but rather to make sure he is doing ok. Calling his client "fragile."
Freund's attorney is also filing a motion for a decorum order, or a gag order, to keep some information about the case sealed.
Cunningham and Freund are expected back in court on June 18th.