The 52-year-old R&B star's lawyer entered the plea for him as he appeared in a Chicago court dressed in an orange jumpsuit.
Kelly remains in jail as he tries to find $100,000 for bail, which his lawyer said friends are trying to arrange.
His plea comes as prosecutors say a bombshell video of him abusing an underage girl is set to be revealed in court.
Lawyer Michael Avenatti claims to be in possession of the 55-minute VHS video and is expected to hand it over to Cook County prosecutors.
The footage is reportedly more disturbing than the first one.
He wrote in a Twitter message: “I can confirm that we will be providing a second video showing R. Kelly engaged in sexual assault of a minor to prosecutors this morning.
“This tape was recently uncovered in connection with our ongoing nationwide investigation on behalf of victims. Justice must be done.”
The new video is said to feature the same girl, thought to be 14, who appeared in the first one, and is believed to have R Kelly “coaching” the girl through various sexual situations.
This second video is believed to have been filmed in 2000, a year after the first one.
Avenatti is also thought to be trying to get hold of a third tape which is said to show R Kelly with a different girl, according to TMZ.
If convicted he faces three to seven years on each count, said Cook County State's Attorney Kimberly Foxx.
He met one of the alleged victims during his 2008 child abuse trial, the judge heard.
'JUSTICE MUST BE DONE'
She is said to have asked for an autograph and allegedly abused the underage girl while the trial was going on.
The 2008 trial stemmed from a video that was said to show him having sex with an underage girl as young as 13. He was acquitted.
Yesterday his lawyer said all his accusers were lying after he was charged with ten counts of aggravated sexual abuse.
Steve Greenberg said Kelly was "extraordinarily disappointed and depressed" and added: "He is shellshocked by this."
The charges came days after campaigning lawyer Michael Avenatti uncovered video that allegedly shows R Kelly having sex with a girl who says on camera she is 14.
The 43-minute tape is said to feature a man "who appears to be R Kelly performing multiple sex acts with the girl", CNN reported.
She and the singer refer to her age ten times, according to reports, and she calls him "daddy".
The man allegedly asks the girl to urinate before he urinates on her, the broadcaster claims.
The prosecution released further details of the allegations against the singer on Saturday.
In one case cited, a 16-year-old who attended his child pornography trial in 2008 got his autograph after a court session.
He is later said to have invited her to his Chicago home where they had sex multiple times, according to the documents, which claimed he also slapped, chocked and spat on her.
Kelly has faced claims of sexual abuse for more than two decades.
Most recently in the Netflix documentary Surviving R Kelly revealed harrowing accounts of his alleged abuse.