Brian Dugan, 49, was charged with 15 counts in the killing of Jeanine Nicarico of Naperville, whose slaying attracted national attention after two men were convicted and sent to death row, then freed years later.
"This is the result of a full and open-minded investigation of the facts and circumstances of this case," DuPage County State's Attorney Joseph Birkett said.
Nicarico was home alone from school recovering from the flu on Feb. 25, 1983, when she was abducted, leaving no sign but fingernail scratches on the wall near the kicked-in front door.
Birkett said Dugan raped and bludgeoned the girl to death. Her body was later found in a nature preserve.
Rolando Cruz and Alejandro Hernandez were convicted of the crime and condemned to death in 1985, but appeals courts over the following decade twice reversed the convictions.
Cruz was acquitted during a third trial in 1995 after spending almost a decade on death row, and prosecutors later dropped the charges against Hernandez.
DNA testing was among the factors that made the indictment possible, Birkett said.
"The past is the past. We're going forward. This indictment is about the evidence available now, today," Birkett said.
He planned to seek the death penalty if Dugan is convicted. "I could not stomach seeing this crime go unpunished."
Thomas McCulloch, Dugan's defense attorney since 1985, said Dugan would probably enter a plea of not guilty.
"I'm saddened but not surprised," McCulloch said of the indictment. "I think it's a terrible waste of time and energy. I wish they spent their time and money elsewhere."
A message left at the home of Jeanine Nicarico's parents was not immediately returned.
After Cruz's acquittal, seven DuPage County prosecutors and law officers were charged in 1996 with lying and fabricating evidence against Cruz in what prosecutors described as a conspiracy to railroad him for the crime. All seven were cleared in 1999 after a high-profile trial.
The case became a centerpiece in the Illinois debate over the death penalty, held up as an example of how people could be sentenced to die on flimsy evidence. Cruz's release was followed by a string of highly publicized cases of men being freed from Illinois' death row after questions arose about their guilt.
That led former Gov. George Ryan in 2000 to halt executions in Illinois, commute the sentences of everyone on death row and propose an overhaul of the death penalty system. Gov. Rod Blagojevich has continued the moratorium on executions.
Dugan emerged as the chief suspect only after Cruz's acquittal, even though prosecutors say he confessed to the crime during a 1985 interview with his attorney while serving a life term for the unrelated rapes and murders of a 7-year-old girl and a 27-year-old woman.
Dugan refused to make a formal confession because prosecutors at the time would not rule out the death penalty in return for a guilty plea.
The same jury that originally convicted Cruz and Hernandez in 1985 failed to reach a verdict against a third man charged in the crime, Stephen Buckley. Charges against him were dropped in 1987.
Cruz, Hernandez and Buckley later sued DuPage County, saying they were wrongfully prosecuted. They settled the lawsuits for $3.5 million in September 2000.