Mr Anwar says the the trial is a political conspiracy The charges, if proven, could send Mr Anwar to jail for 20 years.
Mr Anwar says the charges are a political conspiracy ahead of planned parliamentary elections.
"I find a prima facie case has been made out against the accused, therefore I call upon the accused to enter his defence," Judge Diah told the court.
He said he believed that Mohamad Saiful Bukhari Azlan, the 23-year-old man who accused Anwar of sodomising him, was a reliable witness.
"There is nothing improbable about his evidence. His evidence is reliable," the judge said.
He also found there was evidence that Mr Anwar and Mr Saiful were at the scene of the alleged crime at the time in question and that there was "opportunity for the offence to have taken place".
The judge had earlier reversed a ruling to allow key DNA evidence which had been barred for having been collected illegally when Mr Anwar was held in a police cell.
"It is clear that [Mr Anwar's] arrest was lawful and the detention was for a lawful purpose," the judge said.
The prosecution argues that the DNA from the items would link Mr Anwar to semen found on his accuser, Mr Azlan.
Human Rights Watch has said the charges should be dropped and that the case is a "charade of justice".
Mr Anwar was imprisoned on separate sex and corruption charges in 1998, and freed on appeal in 2004.
Sodomy is illegal in Malaysia, even among consenting adults.
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