Weinstein, 66, wearing a dark blue suit, white shirt and dark tie, answered "not guilty" in a soft voice when asked how he pleaded to the indictment by a Manhattan grand jury last week.
Weinstein was accompanied by defense attorney Benjamin Brafman and surrounded by court officers during the brief hearing in Manhattan Supreme Court. He answered a series of questions from the judge.
"He intends to vigorously defend this case," Brafman said.
The courtroom was filled to capacity. Lawyer Gloria Allred, who represents several of Weinstein's accusers, sat in the second row.
Brafman brought up in court the separate federal civil lawsuit filed last week by three women, including Melissa Thompson, who alleges that Weinstein raped her in a New York City hotel room in 2011. No criminal charges have been filed in connection to that allegation.
But Thompson has also accused Brafman of tricking her into relinquishing evidence of the alleged attack.
Brafman denied knowing Thompson, defended his integrity and assured prosecutors he would "never discourage anyone from cooperating with the district attorney’s office."
Brafman said Weinstein is aware of the allegation and does not believe there is a potential conflict.
Prosecutor Joan Illuzzi said she accepts Brafman’s explanation but asked Supreme Court Justice James Burke to question Weinstein about it, which he did.
"I'm satisfied," Burke said of Weinstein's comprehension of the potential for any conflicts.
Weinstein's next court date is scheduled for Sept. 20. He is free on $1 million bail and his travel is restricted to New York and Connecticut.
He must also abide by a temporary protective order directing him to stay away from the two women whose complaints prompted the charges.
In the meantime, Brafman said he is considering making a motion to split the case in two. He said he hasn’t made up his mind but wanted to consider whether the rape and criminal sex act charges "may require two separate trials."
He also said the case presents "unique issues" that may be the subject of his future motions, but declined to elaborate.
Brafman and Illuzzi briefly sparred over their public statements about the case.
"Mr. Weinstein is presumed innocent," Brafman said as he took issue with how the Manhattan district attorney's office has slammed his criticism of the accusers.
"However reprehensible the crime of rape may be, it is equally reprehensible to falsely accuse someone of rape," Brafman said.
Illuzzi reminded Burke that it was Brafman – not she or Manhattan District Attorney Cyrus Vance Jr. – who spoke on the courthouse steps of how Weinstein did not create the "casting couch."
Brafman promised, "I will never again use the term 'casting couch,'" referring to his previous suggestion that the accusations were more about Weinstein’s questionable behavior than crimes.
Weinstein has been accused by dozens of women of sexual misconduct and has been investigated by the New York City Police Department, the Manhattan District Attorney’s Office, the New York Attorney General’s Office, the Los Angeles Police Department and U.K. authorities. He has denied all allegations of nonconsensual sex.
The criminal sex act charge stems from an allegation brought by Lucia Evans, who has said Weinstein forced her to perform oral sex during what she thought would be a casting call.
The two rape charges stem from allegations by a woman who has not been publicly identified.