Polovin, 48, and Carlos Acosta, 54, have both been charged with endangering the life of a child and reckless conduct.
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The indictments accuse Polovin and Acosta of knowingly permitting AJ to be placed in circumstances that endangered his life.
A lawsuit filed on behalf of AJ Freund's estate accuses these men of failing to fully investigate allegations of abuse against AJ.
RELATED: Crystal Lake home of murdered boy demolished
A status hearing in Polovin's case has been scheduled for October 29. He faces between two to five years behind bars....or probation.
Acosta will be arraigned next week.
A group supporting justice for AJ was present outside the courthouse.
"It's about time," said Tracy Kotzman, a member of the group. "I'm very happy that charges have been filed and I hope they stick."
The Crystal Lake boy was found dead in a shallow grave not far from his parent's home last year. The horrifying child abuse case sparking outrage in the community and calls for DCFS to be held accountable.
RELATED: Andrew Freund, the father of AJ Freund, could reach plea deal this week in murder of Crystal Lake boy
"They failed him," said Rosa Mallette. "No ifs ands or buts about that. He should have been removed from the home."
DCFS declined to comment on the charges against their former employees.
AJ's mother, JoAnn Cunningham, pleaded guilty last December to the Crystal Lake boy's murder. In July, she was sentenced to 35 years in prison.
His father, Andrew Freund, has also been charged. He is due in court on Friday and his attorneys said they are negotiating a plea deal.