The indictment and subsequent arrest warrant, which were unveiled at a news conference at police headquarters, stemmed from a videotape purportedly showing Kelly engaging in sex acts with a 14-year-old girl.
"Criminal conduct, no matter who's involved, will not be tolerated in the city of Chicago," Police Superintendent Terry G. Hillard said.
State's Attorney Richard Devine said investigators are convinced the tape depicts Kelly, despite the entertainer's denials.
The indictment charges Kelly with seven counts each of videotaping, producing and soliciting. The alleged acts took place at Kelly's home.
Kelly was arrested at a home he rents near Haines City, Fla., in Polk County after police had staked out the residence.
"Even though I don't believe any of these charges are warranted, I'm grateful that I will have a chance to establish the truth about me in a court of law," Kelly said in a statement issued in Los Angeles. "I have complete faith in our system of justice, and I am confident that when all the facts come out, people will see that I'm no criminal."
The 26-minute tape was turned over to police Feb. 1 by the Chicago Sun-Times, which received a copy anonymously, and was authenticated by FBI crime lab technicians.
Devine said Kelly should have "known the girl was born in September of 1984 and was a minor." But, he said, investigators do not yet have the evidence to press more severe charges. The investigation is continuing. A second investigation based on allegations made a year earlier also is under way, authorities said.
"These indictments will hopefully send a message to sexual predators that taking advantage of minors will not be tolerated and that there are severe penalties," Cook County State's Attorney Richard Devine said.
The tape, which has been bootlegged, sold on street corners for $10 to $15, and posted for download on Internet Web sites, allegedly shows Kelly having sex with and urinating on the then underage girl in his home. The girl and her parents deny the allegations, as does Kelly.
"The lady in the tape is not who police think she is," Kelly's attorney Ed Genson told WLS-TV. Genson said Kelly was ready to turn himself in.
Police Supt. Terry Hillard said anyone in possession of a copy of the tape would be "well-advised" to dispose of it.
Kelly, 33, could face a 15-year prison sentence and up to a $100,000 fine if convicted of violating child pornography laws.
"If people out there have a tape of me and they're saying it's me and a young girl, a minor ... then they're sadly mistaken, or they're lying ... Nowadays you can make a tape; you can make a song; it can sound like a person or look like a person ... but that's not me," Kelly said in an interview last month on Black Entertainment Television.
Kelly is a true rags-to-riches story. The high school dropout rose from abject poverty, singing for spare change on transit platforms, to become a music superstar with hits that have become Grammy winning standards like 1996's inspirational "I Believe I Can Fly," from the "Space Jam" soundtrack.
His five albums have sold more than 23 million copies, and the Grammy winning TP-2.com album debuted at No. 1 in November 2000.
According to the Sun-Times, after he become a superstar, Kelly often cruised around his old high school picking up young girls. Tiffany Hawkins charged Kelly coaxed her to engage in group sex with him and other underage girls when she was 15. Her lawsuit was settled out of court for $250,000.
Kelly has two daughters and a month-old son with his second wife Andrea, 28, a former dancer in his touring group. His first wife was the late pop star Aaliyah, who lied about her age to marry Kelly in a secret ceremony in 1994, when she was only 15. The marriage was annulled in Detroit less than six months later.
Aaliyah Haughton died in a plane crash last August while shooting a music video in the Bahamas.
Kelly negotiated settlements with several young women who either filed lawsuits or threaten to, including 16-year-old Tracy Sampson, who said Kelly picked her up in a McDonald's the night of her senior prom. Montina Woods, 33, became the fifth woman to sue Kelly in May, claiming the singer secretly videotaped her performing sex acts with him in his studio.
The allegations may be hurting Kelly's popularity. Community activists and religious leaders in Chicago, New York, Philadelphia, Atlanta and Los Angeles urged a boycott of radio stations and stores that promote his music and his recent collaboration with rapper Jay-Z, "The Best of Both Worlds," sold poorly. Jay-Z refused to tour or to be photographed with Kelly.
"I believe what Robert Kelly has done is a crime," said Rev. Bamani Obadale, a black minister who derided adult men who take advantage of young girls.
He said giving R. Kelly a pass on the allegations "says to young people 'Well, it's OK."
However, Howard McGee, a popular morning DJ on WGCI-FM radio, said the station would continue to play Kelly's songs until he was proven guilty.