The singer appeared before Cardiff Crown Court, south Wales, on Monday in a plea hearing via video-link.
Two women, aged 20 and 24, also denied sexual offences against children. Both appeared via video-link. Neither can be named for legal reasons.
Watkins, 35, of Pontypridd, south Wales, denied 23 separate charges, among them for the first time two allegations he raped a baby, aged one at the time.
One of the two women allegedly involved is accused of aiding and abetting him to carry it out.
Watkins, whose band has sold more than 3.5 million albums worldwide, is also accused of aiding and abetting the sexual assault of a child.
He also faces a series of charges for possessing, making and distributing indecent images of children.
He is also accused of possessing extreme images depicting a person having sex with an animal.
The oldest of the alleged offences dates back to 2007.
The clerk in court on Monday confirmed after the hearing that Watkins had pleaded not guilty to all charges.
She confirmed that he appeared via video-link from where he is being held in custody at Parc Prison, Bridgend.
She added that both he and the two women are collectively accused of a total of 32 offences. All three deny all the charges.
Recorder of Cardiff judge Eleri Rees adjourned proceedings until Thursday for a case management hearing at the same court.
Legal teams from all sides are expected by then to know the availability of expert witnesses integral to their cases.
Judge Rees is expected to be able to set a date for the eventual trial of Watkins and the two women.
All three remain remanded in custody.
In December the members of Lostprophets spoke of their "shock" after Watkins was charged.
In a statement on the band's website signed by Jamie, Lee, Luke, Mike and Stu, the band thanked fans for their support and said they were in a "state of shock."
"We are learning about the details of the investigation along with you. It is a difficult time for us and our families, and we want to thank our fans for their support as we seek answers," the message said.
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