He entered a not guilty plea on Wednesday.
Earlier this month, the Justice Department added a charge of bribery against Kelly, accusing him of obtaining a false ID for an unidentified woman in 1994, reports cnn.com.
The New York Times, citing a person familiar with the matter, reported that Jane Doe was singer Aaliyah, who was 15 years old and whom Kelly married later that year.
The singer appeared in the Chicago courtroom with lawyer Steve Greenberg and spoke only to greet the judge from the Eastern District of New York and to confirm he understood the superseding indictment.
After the hearing, another of Kelly's attorneys said that the singer maintains his position that the updated indictment is "ridiculous."
Attorney Douglas Anton said his client is doing well and is writing "uplifting" lyrics while in jail.
In July, Kelly was charged in New York in an indictment that accused him of violating federal law by coercing and transporting women and girls across state lines to engage in illegal sexual activity.
He pleaded not guilty in August to a slew of charges including counts of racketeering, kidnapping, forced labour and sexual exploitation of a child in a court in Brooklyn.
Aaliyah Haughton burst onto the R&B music scene as a 15-year-old protégée of Kelly.
Their marriage was annulled in 1995 after Aaliyah's family became aware of it, the
Chicago Sun-Times had reported.
Aaliyah became a multi-platinum selling artist and launched a movie career with roles in "Romeo Must Die" and "Queen of the Damned."
She was killed in a plane crash in August 2001.
( With inputs from IANS )