The judge scheduled a probable cause hearing for Oct. 20, in which sides will have the right to introduce evidence and call witnesses. Under Connecticut law, defendants accused of murder have the right to the hearing within 60 days of their arrest to decide if the case will go forward.
Under state law, defendants charged with crimes punishable by death or life in prison do not enter a plea before a judge determines there is probable cause to believe they committed the crime. Defendants may waive their right to a probable cause hearing.
Clark's attorney, Joseph Lopez, said his client will plead not guilty after they decide whether to waive his right to a probable cause hearing.
The judge said he will also consider at that hearing whether to extend a sealing order on the police arrest affidavit in the case.
Le was a pharmacology graduate student who vanished Sept. 8 from a Yale medical lab building. Her body was found in the building five days later, on what was supposed to have been her wedding day.
Police have not talked about a motive in the slaying, largely because Clark has not talked to authorities. Investigators and Yale officials have called Le's death a case of workplace violence, but have not elaborated.
Co-workers have told police that Clark was controlling and viewed the laboratory and its mice as his personal fiefdom.
As a technician, Clark's duties included cleaning mouse cages and the floors of the lab.
Le's work involved experiments on mice that were part of research into enzymes that could have implications for the treatment of cancer, diabetes and muscular dystrophy.
Security cameras at the medical school research building recorded Le entering the morning of Sept. 8, and investigators initially were baffled that there was no record of her leaving.
Her body was found Sept. 13 in the basement laboratory in a wall chase - a hidden access that allows utility pipes and wires to run vertically between floors.
Investigators, who had been keeping around-the-clock surveillance of Clark, labeled him a person of interest two days later and got a court order to take forensic evidence from him and search his apartment. Clark was arrested Sept. 17 after DNA evidence linked him to Le's body.
He has been jailed since his arrest. A judge set his bond at $3 million.
Meanwhile, Yale officials said they are examining whether health records were improperly accessed by staff at Yale University Health Services after Le disappeared, according to spokesman Tom Conroy. He would not say if they were Le's records.
"If the investigation confirms there was inappropriate access of patient records, severe disciplinary action will be taken up to and including termination," Conroy said in a statement.