Last week, the singer was indicted on multiple federal charges in Chicago and New York, where a separate indictment returned in Brooklyn accuses him of racketeering and sex trafficking.
RELATED: R Kelly facing charges in New York City
Dressed in an orange jumpsuit with his ankles shackled, the only words Kelly spoke were "yes sir" when he told the judge he understood the charges against him.
Federal Judge Harry Leinenweber called the charges "extraordinarily serious" as he denied Kelly's bond.
Kelly's attorney Steve Greenberg said he had been expecting to get the singer released on bond Tuesday, and said they are now evaluating their options.
Kelly has been in jail since he was arrested while walking his dog last week near his Trump Tower apartment in Chicago.
Greenberg tried to argue his client is not a flight risk because he is broke, has always shown up for court cases in the past and, according to Greenberg, does not like to fly. But federal prosecutors called the 52-year-old an extreme danger to humans, especially minor girls.
As part of the indictment filed in Chicago, Kelly has been charged with one count of conspiracy to receive child pornography, two counts of receiving child pornography, four counts of producing child pornography, five counts of enticement of a minor to engage in criminal sexual activity, and one count of conspiracy to obstruct justice.
Federal prosecutors allege Kelly sexually abused a dozen women and girls, some as young as middle school. Prosecutors also argued Kelly is a serious risk for obstruction of justice. He is accused of paying off witnesses in his 2008 case and paying hundreds of thousands of dollars to recover sex tapes.
"He's facing charges that, when you look at the Cook County case and two federal cases, he's really looking at life in prison if he is convicted on all of these," said criminal defense attorney Andrew Weisberg. "I think he becomes too much of a flight risk in theory. Also, I've heard he may be a continuing danger to the public. I think for those reasons, the judge is going to deny his right to post bail."
Two of Kelly's girlfriends were there to support him in court. Their parents claim they have been brainwashed by Kelly.
In the second indictment out of Brooklyn, New York, Kelly is charged with racketeering, including acts of coercing and transporting minor girls to engage in sex, spanning two decades in New York, Connecticut, Illinois and California. Prosecutors said he was at the center of an "enterprise" to recruit women and underage girls.
RELATED: R. Kelly arrested by NYPD in Chicago on federal sex crime charges including child pornography, obstruction of justice
Kelly is already facing sexual abuse charges brought by Illinois prosecutors earlier this year. He was taken into custody in February, accused of sexually abusing three girls and a woman in Illinois.
In May, Cook County prosecutors added 11 more sex-related counts. Kelly has maintained his innocence and pleaded not guilty to the Illinois charges.
Hearing in R. Kelly case to be held Tuesday after singer charged with federal sex crimes
R. Kelly appears in court on federal sex crime charges
R. Kelly arrested by NYPD in Chicago on federal sex crime charges including child pornography, obstruction of justice
R. Kelly pleads not guilty to new sexual assault charges
RELATED: Chicago reporter makes his case against R. Kelly in new book
RELATED: R. Kelly pleads not guilty to new sexual assault charges
RELATED: R. Kelly: New charges 'raise the stakes,' attorney says
RELATED: R. Kelly facing 11 new counts of sex charges in Chicago
R. Kelly pays $62K in back child support; Judgement in lawsuit vacated after Kelly's lawyers say singer can't read
R. Kelly appears in court Tuesday for status hearing
RELATED: R. Kelly performs for 28 seconds at Springfield club; fans upset
RELATED: R. Kelly's attorney appears in court
RELATED: Dubai denies there were plans for R. Kelly concert
RELATED: R. Kelly appears in court Friday
RELATED: R. Kelly will request permission to travel to Dubai via private jet for concerts
RELATED: R. Kelly appears in court for child support hearing
RELATED: R. Kelly released from Cook County Jail
RELATED: Man says he found videotape of R. Kelly sexually abusing girls
RELATED: R. Kelly in jail for failing to pay child support; New allegation surfaces
RELATED: R. Kelly returns to jail for failing to pay child support
RELATED: R. Kelly speaks publicly for 1st time since new sex abuse charges
RELATED: 'Friend' who posted bail for R. Kelly identified
RELATED: R. Kelly released from jail after pleading not guilty to sex abuse charges
RELATED: 'I'm the one you ignore': Chicago writer tenacious in R. Kelly coverage that has spanned years
RELATED: R. Kelly remains in jail; singer's finances 'a mess,' lawyer says
RELATED: R. Kelly charged: A look back at key moments of the singer's life and career
RELATED: R. Kelly charged with 10 counts of sex abuse, bond set at $1M
RELATED: R. Kelly looking at jail without bond, life in prison if convicted
RELATED: R. Kelly charged with 10 counts of sex abuse, in police custody
RELATED: R. Kelly moving out of West Side studio
RELATED: R. Kelly lawyer disputes report that grand jury convened to examine allegations against singer
RELATED: Allred concerned client may be on R. Kelly tape
RELATED: R. Kelly seen having sex with underage girl in new tape, attorney says
RELATED: Keys from Atlanta TV crew's rental car stolen outside R. Kelly's studio
RELATED: Judge rules R. Kelly can't use West Loop recording studio overnight
RELATED: SEE INSIDE: R. Kelly hasn't cleared bedroom from West Loop studio, inspectors say
RELATED: SEE INSIDE: Judge orders clean-up, new restrictions at R Kelly's studio
RELATED: R. Kelly attorney speaks out after singer's West Loop studio inspected
RELATED: A look inside R. Kelly's West Loop studio; city inspectors find violations
RELATED: City inspectors find violations at R. Kelly's West Loop studio
RELATED: Alleged victim accuses R. Kelly of trying to silence her
RELATED: City to inspect R. Kelly's Near West Side music studio
RELATED: Lady Gaga apologizes for R. Kelly collaboration
RELATED: R. Kelly parties at South Side nightclub as legal pressures mount
RELATED: Protesters call for prosecution, boycott of R. Kelly outside Chicago studio
RELATED: Foxx asks for cooperation from possible victims, witnesses to open R. Kelly investigation
RELATED: Chance the Rapper apologizes for past work with R Kelly
RELATED: R Kelly's accusers, inner circle revisit shocking allegations in new docuseries
RELATED: R. Kelly's ex-wife shares story of abuse, survival ahead of documentary