Madison County prosecutors charged the man, Kevin Reid, on Friday with two counts of first-degree murder, one count of intentional homicide of an unborn child and two counts of concealment of a homicidal death.
No other details were immediately released. A news conference was set for Friday afternoon.
Earlier, state police said they were awaiting forensic testing that could confirm the skeletal remains found Wednesday were Anquiaette Parker, 19, of East St. Louis and her cousin Cermen "C.J." Toney Jr.
The young woman and her cousin disappeared in November 2005 while she was baby-sitting for the boy. The disappearance prompted vigils and dozens of searches.
The remains were found in an unincorporated area roughly a quarter of a mile from where Parker's car was found shortly after her disappearance.
"Yesterday, I felt in my heart it was over. It's a relief," Greg Parker, Anquiaette's father, said Thursday. "I had faith in finding them, but we've got closure now."
Men using a bulldozer to clear the site of weeds partly broke through a cistern, saw the remains and called authorities, state police Lt. Mark Bramlett said. Investigators converged on the site and removed evidence Bramlett said was sent to a state police crime laboratory.
The property, near the Fairmount Park horse racing track, includes a battered home with many of its windows boarded up.
