The documents say that a grand jury considered charges against the child's parents, John and Patsy Ramsey.
The Ramseys were cleared of wrongdoing years ago through examination of DNA evidence.
The district attorney at the time declined to pursue charges, saying there was not enough evidence.
The case captured attention around the world.
Her case is still unsolved, but now documents from a grand jury that convened three years after her death, say jurors wanted to indict both her parents of child abuse leading to death, accusing them of hindering the investigation and helping whomever killed their daughter.
"Grand jury did not indict for murder, the grand jury indicted for child abuse resulting in death. Which is easier to prove," said former Denver County District Attorney Norm Early.
The grand jury's burden of proof is lower than what's required for a district attorney to file charges.
After the investigation, the D.A. at the time announced he had no case.
"We do not have sufficient evidence to warrant the filing of charges against anyone who has been investigated at this time," Alex Hunter said.
The Ramseys repeatedly maintained their innocence.
Patsey Ramsey died of cancer in 2006.
Two years later, a D.A. exonerated both of them, based on new DNA evidence pointing to an unknown male suspect, not a family member.
Daily camera reporter Charlie Brennan and other journalists filed suit over the public's right to know about the indictment.
John Ramsey earlier this week asked the court to release the entire grand jury record, if the unprosecuted charges would be made public.
But the judge ruled to release only the indictment, despite arguments it would further.
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