The charges came on the same day Jason Quate was told he would remain jailed without bail in Las Vegas, where he is accused of forcing his wife into prostitution and abusing their two other daughters.
Mr Quate stood in shackles and answered "Yes, sir," when a local judge asked if he understood he was charged with felony sex trafficking and living from the earnings of a prostitute.
He wasn't asked to enter a plea, but his court-appointed lawyer, Katrina Ross, said outside court that he will plead not guilty. Ross declined to comment about evidence in the case.
The judge said Mr Quate's lawyer could file documents seeking his release, but that he will remain held without bail pending a June 22 preliminary hearing to determine if there is enough evidence to order him to stand trial in state court. Convictions on both charges could get him up to 24 years in prison.
Coroner Calvin Dye Sr in St. Clair County, Illinois, said on Friday that the child's body was too decomposed for an autopsy to immediately determine how she died.
He said further testing would be necessary on the bones, and that results might not be known for a couple of weeks.
Mr Quate also faces child abuse and child pornography charges in separate cases filed in Las Vegas following his arrest on Tuesday. Prosecutor Samuel Martinez said Mr Quate's initial appearances are expected Monday in separate courts on those cases.
The mother has been jailed in Las Vegas pending a court appearance on Monday as a fugitive on an unspecified out-of-state warrant.
It was not immediately known if that case was connected with the discovery of her daughter's body.
The Associated Press is withholding the woman's name to avoid identifying the couple's now-teenage children and because authorities said she was considered a victim in the sex trafficking and prostitution case. She has not been charged with a crime in Las Vegas.
Jason Quate has given differing accounts about his daughter to some media. He declined jailhouse interview requests from The Associated Press.
Mr Quate told the St Louis Post-Dispatch the girl choked to death with food in her mouth when he spanked her, and his wife found the place to hide the body.
He told KSNV-TV in Las Vegas that his wife told him she put the girl up for adoption. But he also told the Post-Dispatch that he lied to the TV station and that his wife concocted the adoption story.
The family moved to Las Vegas in January 2016, according to a police report obtained on Friday. Police said Mr Quate had acknowledged that his wife worked as a prostitute, but denied that he was her pimp.
Mr Quate described himself to investigators as a stay-at-home dad, the report said. Police have said their two daughters were never allowed outside their apartment, even to attend school. The girls have been placed in protective custody.
- Associated Press writer Jim Salter in St Louis contributed to this report.
