Weinstein still faces almost a dozen lawsuits filed by some of the 80 women who have accused him of sexual assault and harassment.
The new charges stem from accusations that Weinstein forcibly performed oral sex on a woman in July 2006.
Movie mogul Harvey Weinstein pleaded not guilty on Monday to charges of sexually assaulting a woman in 2006, the third criminal sex assault case brought against him, and his attorney said he expects further charges to follow.
The 66-year-old was brought into NY state Supreme Court wearing handcuffs, but he was uncuffed during proceedings.
The new charges include two counts of predatory sexual assault, which carries a maximum sentence of life imprisonment.
"Mr Weinstein maintains that all of these allegations are false and he expects to be fully vindicated", Mr Brafman said.
Weinstein, who wore a black suit and tie, has been out on $1 million bail and staying at his longtime family home in CT in recent months. "He is not a rapist and I believe that when this case is over, we will ultimately see him to be exonerated", Brafman said after the hearing.
"A Manhattan Grand Jury has now indicted Harvey Weinstein on some of the most serious sexual offenses that exist under New York's Penal Law", Manhattan District Attorney Cyrus R. Vance Jr. said in a statement.
Among those in the courtroom was Gloria Allred, who has represented several of Weinstein's victims.
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More than 75 women have accused Weinstein of wrongdoing as allegations detailed in Pulitzer Prize-winning stories last October in The New York Times and The New Yorker magazine swelled into the #MeToo movement.
Former actress Lucia Evans told The New Yorker that Weinstein forced her to perform oral sex and is thought to be one of the women.
Since then, more than 40 women, including actresses Ashley Judd, Gwyneth Paltrow and Angelina Jolie, have accused Weinstein of sexual misconduct.
Sopranos actress Annabella Sciorra, who alleged he raped her in her NY apartment in 1992.
A former Weinstein Company production assistant, Mimi Haleyi, last October made allegations against Weinstein that align with the charges in the updated indictment.
The 66-year-old has denied all charges of non-consensual sex.
One of the other two accusers, who has not been identified publicly, told investigators Weinstein allegedly cornered her in a hotel room and raped her in 2013. Dozens of women have come forward in recent months to accuse the producer of assaulting or harassing them.
Weinstein, the producer of hit indie films such as "Pulp Fiction" and "Shakespeare in Love", was a force in Hollywood, renowned for his ability to pick art house fare that could cross over into the mainstream, and feared for his volatile temper.
"Mr Weinstein is not a predator".