Thompson claimed to be indigent and was appointed a public defender.
Thompson's indictments were unsealed at his court appearance on Thursday. Formore details on the 60 counts, click here.
A grand jury which investigated the case for a year indicted Thompson Wednesday for charges related to the death of the girl.
Amongst the60 counts,Thompson faceschild abuse resulting in death -knowingly or recklessly, multiple counts of conspiracy to commit child abuse resulting in death, false reporting to authorities, concealing death, conspiracy to conceal death, abuse of a corpse, conspiracy to commit abuse of a corpse, multiple counts of contributing to the delinquency of a minor, and multiple counts of child abuse resulting in injury.
Thompson was arrested in Aurora just after 12:30 p.m. Wednesday and his bond was set at $500,000. He will be back in court on May 29.
"Aaron Thompson has consistently said that he's had no knowledge of or involvement in the disappearance of Aarone," said David Lane, Thompson's attorney.
Aarone's mother spoke with 9NEWS after Aaron Thompson's arrest.
Lynette Thompson says she wants to know where her daughter is so she can bury her.
"She was a busybody, she had spunk, she was loveable, you would have loved her, loved to play, loved to talk," said Lynette Thompson on Wednesday.
Aaron Thompson is facing serious charges, according to 9NEWS Legal Analyst Scott Robinson.
"It's much easier to prove child abuse resulting in death. You don't have to prove after deliberation. You don't have to prove anything except willful or knowledgeable conduct causing the death of a child under the age of 12 by a person of trust," said Robinson.
He says it's equally serious that it is part of a grand jury indictment.
"The fact that this is a grand jury indictment is very significant. That means that at least nine out of 12 grand jurors thought there was probable cause to indict," said Robinson.
Thompson, 39, had reported the 6-year-old missing in November 2005, claiming she ran away after an argument over a cookie.
More than 100 police officers and volunteers searched for Aarone, and Thompson made tearful pleas for the safe return of his daughter.
Yet within days, investigators labeled the case as a homicide, and named Thompson and his girlfriend, Shely Lowe, as persons of interest. The case concerned them because there were no credible reports of Aarone being seen for at least 18 months prior to the time she was reported missing, police said, and the mattress from her bed in the Thompson home was gone.
In addition, information from Lowe's former common-law husband, Eric Williams, implicated the couple.
Williams told police Lowe had confided to him the girl was killed in the family home and buried in a field by Thompson and Lowe, according to court records.
Seven other children living in the home were removed by social services, as well as an infant child born later to Thompson and Lowe.
After the couple went to court for custody, a ruling that Aaron Thompson "was responsible for serious bodily injury or the death" of his daughter, Aarone, was issued by the state Court of Appeals.
The court affirmed the decision made by a dependency and neglect jury.
In the decision issued February 8, the Colorado Court of Appeals said "the record contains sufficient competent evidence" that then 6-year-old Aarone Thompson, reported missing by her father and his girlfriend, Shely Lowe, in Nov. 2005, "…went missing long before reported by the parents, that the parents were not forthcoming about the circumstances of her disappearance, that the parents did not want the children to talk to police, and that the child was probably deceased."
"This is so devastating," Lynette Thompson, Aarone's mother, told 9NEWS at the time from her home in Detroit, Michigan. "Oh my God, you mean to tell me that he killed his own daughter? That's not the man that I married."
Lowe and Thompson had asked to have the dependency and neglect case heard by a jury, and after a nine-day trial, the jury returned special verdicts "finding that the children were dependent or neglected."
In addition, court records said, "In response to a special interrogatory, the jury also determined that father was responsible for serious bodily injury or the death of A.T. due to proven parental abuse or neglect."
Based on that finding, "an appropriate treatment plan could not be devised to address father's unfitness."
Lowe died in May 2006 of heart problems, shortly before the grand jury was convened to hear the case.
