Beale pleaded not guilty to one count of sexual intercourse without consent and two counts of sexual touching when he appeared at the Downing Centre District Court on Thursday.
A further charge of inciting another to sexually touch the alleged victim was withdrawn by prosecutors.
Beale, who is on bail, is accused of sexually assaulting a 28-year-old woman at a licensed premises near Bondi Beach on December 17.
The matter will come before the District Court on July 14 where further steps will be made to set down the trial.
Magistrate Susan Horan also continued an interim AVO against the rugby star with this coming back before the courts on November 15.
On that date, a judge will consider whether the AVO needs to be continued in light of the verdict at trial.
Outside court, Beale told reporters he was devastated to be there.
"I'm not guilty. The allegation has been falsely (brought) against me and the truth will come out," he said.
The Waratahs and Wallabies back has played 95 games for Australia.
He won the 2011 John Eales medal for player of the year.
Rugby Australia has suspended Beale from all forms of rugby as the case continues.
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