His lawyer said Kelly had been re-indicted in his existing case for being a suspected victim.
The charges range from aggravated sexual assault, criminal sexual assault to harder sexual assault, according to the document.
A person convicted of aggravated criminal sexual assault may be sentenced to between six and 30 years of imprisonment under the laws of Illinois.
Kelly, 52, has vehemently denied any allegations of sexual misconduct.
A crisis manager for Kelly, Darrell Johnson, said, "He still clings to his innocence and denies all allegations made against him by (the alleged victim), and looks forward to a quick and swift process."
His lawyer said the new indictment changed "nothing."
"It's the same behavior, only charged differently, the same alleged victim, the same time frame, the same facts, we expect the same results," tweeted defender Steve Greenberg.
Kelly is scheduled to appear in court on June 6, said Sophia Ansari, a spokeswoman for the Cook County sheriff's office.