Kelly, 52, faces 10 counts of aggravated criminal sexual abuse, according to the Cook County State's Attorney's Office in Chicago.
A judge issued a warrant for the singer's arrest on Friday afternoon.
The indictment released on Friday listed four victims, at least three of whom were under 17 at the time they were allegedly victimized by Kelly. They were identified only by initials in the court papers.
The alleged sex acts occurred between May 1998 and January 2010, prosecutors said.
Cook County State’s Attorney Kim Foxx read Kelly's indictment during a brief news conference but left without answering any questions.
A bond hearing for Kelly is scheduled for Saturday afternoon, and his arraignment is set for March 8.
He faces up to three to seven years in prison for each charge if convicted.
Requests for comment to Kelly's Chicago-based lawyer were not returned.
Kelly, whose real name is Robert Kelly, has been criminally accused of sexual misconduct before. He was tried on child pornography charges in 2008. A jury cleared him on all counts.
But allegations of sexual misconduct against the singer gained renewed attention this year with the airing of a Lifetime docuseries "Surviving R. Kelly" in early January.
The six-part show contains interviews with numerous women who accuse Kelly of mental, physical and sexual abuse. Sony Music parted ways with the Grammy-winning artist in the wake of "Surviving."
The singer and his lawyers have consistently denied any wrongdoing in previous allegations made against him over the years.
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