The body, believed to be that of Andrew "AJ" Freund, was covered in plastic and buried in a shallow grave in a rural area of Woodstock in McHenry County, Crystal Lake police Chief James Black said.
Black said investigators went to the site after they interviewed the boy's parents overnight and presented them with cellphone evidence. Woodstock is about 50 miles (80 kilometers) northwest of Chicago and a few miles from the family's home in Crystal Lake.
"This is not the outcome that we want to talk about ... but it is the unfortunate result," said Jeffrey Sallet, who runs the FBI in northern Illinois.
The parents, Andrew Freund Sr. and JoAnn Cunningham, each face charges of first-degree murder and other crimes. An email seeking comment was sent to Cunningham's lawyer. It wasn't immediately known if Freund has a lawyer.
The couple reported AJ missing last Thursday, telling officers they had last seen him at bedtime the previous night. Freund told a dispatcher that they'd checked "closets, the basement, the garage, everywhere," but investigators quickly knocked down the possibility of a kidnapping.
Speaking to reporters, Black had a message for AJ's relatives: "It is my hope that you may have some solace in knowing that AJ is no longer suffering and his killers have been brought to justice."
Crystal Lake police had visited the house over the years, according to records released by the department. One report described the home as littered with dog feces and urine, including a child's bedroom where the "smell of feces was overwhelming." Another report said the house was "cluttered, dirty and in disrepair," and sometimes without electricity.
The Illinois Department of Children and Family Services, known as DCFS, had contact with the family since AJ was born with opiates in his body in 2013. The Northwest Herald said he was in foster care for two years before being returned to his parents. A younger brother was removed from the home last week.
Black said the cause of AJ's death remains under investigation. Police removed several items from the home, including a shovel, mattress, paper bags and a plastic storage tub.
"We know you are at peace playing in heaven's playground and are happy you no longer have to suffer," the police chief said in a public message intended for the boy.
DCFS acting director Marc Smith said AJ's death was "heartbreaking."
"The department is committed to conducting a comprehensive review of the entirety of our work with Andrew's family to understand our shortcomings and to be fully transparent with the public on any steps we are taking to address the issues," Smith said in a written statement.
Gov. J.B. Pritzker in March ordered an independent review of DCFS after the deaths of a 2-year-old girl in Decatur and a 2-year-old boy in Chicago. Child welfare workers had contacts with both families.
State Sen. Julie Morrison, a Deerfield Democrat, immediately called for "an independent, comprehensive audit of the DCFS hotline."
"As with many other deaths, it seems the system designed to protect Illinois' children did not work in AJ Freund's case," Morrison said in a statement.
Copyright 2019 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.