The singer is known for songs such as Ignition and I Believe I Can Fly
R Kelly has been charged with 10 counts of aggravated criminal sexual abuse, at least nine of which involve minors.
The R&B star, whose real name is Robert Sylvester Kelly, has faced decades of claims of sexual abuse against women and teenagers below the age of consent.
He has never been convicted and has previously denied other allegations.
An arrest warrant was issued, and the 52-year-old turned himself in to police in Chicago later on Friday. His lawyer says he is “shell-shocked”.
Steve Greenberg told The Associated Press that his client was “extraordinarily disappointed and depressed” by the charges and maintains his innocence.
The indictment come just weeks after a documentary series called Surviving R Kelly aired.
It contained decades of allegations of abuse against R Kelly, from many women, including the singer’s ex-wife.