The Hollywood producer appeared in court in New York after he was charged last month with two counts of rape and one of a criminal sexual act.
The alleged incidents involve two separate women in 2004 and 2013.
Dressed in a black suit jacket and tie, Weinstein, 66, quietly answered a series of yes and no questions from a judge asking if he understood his rights at the hearing in Manhattan.
His lawyer Benjamin Brafman said the defence team is set to “begin our fight” in the courtroom following Weinstein’s not guilty pleas.
He added that Weinstein was “holding up reasonably well” and the case against the producer was “eminently defensible” based on what they have learned about the evidence.
One alleged victim has told investigators that Weinstein cornered her in a hotel room and raped her.
The other accuser, former actress Lucia Evans, who has waived her right to anonymity, alleges that Weinstein forced her to perform a sexual act at his office in 2004.
Weinstein, who has denied all allegations of non-consensual sex, is due back in court on 20 September.
He turned himself in at a New York police station on 25 May and he was taken to court in handcuffs for his initial arraignment.
At that time a judge released Weinstein on $1m cash bail on the condition that he surrender his US passport and agrees to wear a location-tracking device.
He was also ordered to remain in New York state or Connecticut.
Dozens of women have accused Weinstein of sexual misconduct ranging from harassment to assault, with the scandal sparking the #MeToo movement.
His lawyer has challenged the credibility of his alleged victims and says his client is confident he is going to clear his name.
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Mr Brafman has previously called the rape allegation “absurd,” saying that the accuser and Weinstein had a consensual sexual relationship that continued after the alleged 2013 attack.
Weinstein was fired as chief executive of the Weinstein Company after the allegations emerged last year, and his wife is in the process of divorcing him.