The remains, discovered during a search for three missing teenagers, were found covered in heavy layers of plastic and duct tape. Police used a jackhammer and hand tools to locate and remove the bodies from the concrete.
The suspect, David E. Maust, 49, has been in police custody since Tuesday. He had gone to prison for the 1981 murder of a 15-year-old Illinois boy but was released in 1999.
Maust is scheduled for an arraignment on Friday.
Coroner David Pastrick identified the victims as Michael Dennis, 13; James Raganyi, 16; and Nick James, 19.
Holes were first drilled through the 12-inch thick concrete last Friday. Further digging Tuesday revealed two bodies, wrapped in plastic and tied with cords and tape, a police affidavit said. The third body was removed Wednesday.
Dennis and Raganyi were last seen Sept. 10 at a home near where Maust lived in this northwestern Indiana city. The two teens were friends and had visited Maust in his second-floor apartment, a friend of theirs told detectives.
James, the 19-year-old, died of blunt trauma to the head, Pastrick said, but strangulation or suffocation are the suspected causes of death for the younger teens.
Police Chief John Cory said Maust has confessed to strangling Raganyi with a rope while drinking alcohol with the teen Sept. 10.
Detectives are expected to continue working in the house for most of the weekend collecting evidence.
"We drilled holes in the freshly poured concrete. A cadaver dog was brought out and did not hit on any additional spots in the basement," Sgt. Christopher Matonovich, a police spokesman, told reporters Thursday. "We feel we dug up what we could and there are no more bodies in the basement."
Officers have also searched in and around the two-story apartment house using ground-penetrating radar equipment, Cory said. Tarps were hung between the house and the home next door, and newspapers covered a first-floor window to block views of the search.
The site of the search is just north of downtown Hammond, in a neighborhood of tightly packed, dilapidated homes. City officials said they have battled gang activity in the area and installed high-powered streetlights in an attempt to curb crime.
Cory would not say whether Maust had talked about the deaths of Dennis and James, or whether investigators suspect anyone else was involved in the slayings. Lake County Prosecutor Bernard Carter declined to say whether any sexual abuse was involved.
Various media reported that Maust pleaded guilty to killing a 15-year-old boy near Elgin, Ill., in 1981. Sentenced to 35 years in prison, he was paroled four years ago.
Maust made sexual advances toward the boy at an abandoned quarry, then stabbed him in the abdomen, threw him in the water and held his head under until he drowned, according to the reports, which quoted court records.
When he was charged with the Illinois murder, Maust was serving a five-year sentence in a Texas jail for stabbing a child.
Phil Bettiker, a former Cook County (Ill.) sheriff's investigator, dealt with the 1981 case.
"I would like to have seen him go away for a longer time" for that killing, Bettiker said. "I think he's gone this time."
By Tom Coyne