The rape charges against the four are punishable by up to 40 years in jail.
It was the first public appearance by Lance Corporals Daniel Smith, Keith Silkwood and Dominic Duplantis and Staff Sergeant Chad Carpentier since the alleged November 1 rape of a 22-year-old Philippine woman.
Judge Benjamin Pozon earlier threw out a Justice Department motion to reduce charges against the four and kept all of them as principal defendants.
Silkwood’s lawyer, Jose Justiniano, said the defendants’ entering of a plea may be considered a waiver of their right to appeal the decision not to downgrade any charges.
“We will file a petition ... with the Court of Appeals questioning that ruling,” he said.
The marines, who wore civilian clothes, have been in the US embassy’s custody.
Journalists were barred from the courtroom, but peered in through windows.
The four marines were whisked away after the charges were read. !
Women’s group Gabriela demonstrated outside the courthouse.
The defendants belong to a force stationed on the southern Japanese island of Okinawa. They had finished manoeuvres with Filipino troops when the alleged rape occurred in a van at a former US naval base near Olongapo, west of Manila.
The US Embassy has refused to turn them over to Philippine police, citing a provision under the Visiting Forces Agreement that lets US authorities hold American servicemen facing a criminal case. US officials have refused to disclose their hometowns.
Former vice-president Teofisto Guingona, a prosecution lawyer who has opposed the US military presence in his country, asked the court to issue arrest warrants for the marines and to detain them in a Philippine jail.
The court did not immediately grant his request. The judge cited an earlier Supreme Court ruling on the VFA’s constitutionality.
Private prosecutions have questioned the constitutionality of the VFA — particularly one setting a one-year limit, starting from the arraignment, on a trial of US suspects.
Private prosecutor Evalyn Ursua said the judge has not yet ruled on these issues.