The issue of whether Bernard Thomas Jr. intentionally killed a 19-year-old woman after an alleged sexual assault 34 years ago will be a subject of intense pretrial talks with prosecutors, his attorney said after the arraignment this week.

Thomas — who has been arrested 56 times — pleaded not guilty to three counts of felony murder in the shooting death of Michelle Dixon in a case that Buffalo’s Cold Case Squad recently reopened.

Dixon was found facedown in her bed, with a pillow over her head and small-caliber bullet wounds in her head and back May 20, 1975.

Thomas was arrested May 18 after Cold Case detectives took another look and found DNA evidence they said linked Thomas — a Dixon family friend — to the crime. Thomas, 55, of South Division Street, was indicted by an Erie County grand jury last week. He is accused of killing Dixon in her Carl Street home while her mother and brother were elsewhere in the residence.

After Tuesday’s arraignment, Joseph A. Agro, Thomas’ court-appointed attorney, said his client has always admitted that he had sex with Dixon before she was shot. But Agro, confirming that Thomas has always been the sole suspect, predicted that the case “is going to come down to whether he intended to kill her.”

Thomas is charged with second-degree, or intentional, murder, along with two counts of murder while committing felony sex crimes. Those counts, court officials said, involve allegations that Thomas had sexually assaulted and then sodomized the victim before killing her.

Homicide prosecutor Gary W. Hackbush and Erie County District Attorney Frank A. Sedita III declined to comment on Agro’s post-arraignment statements.

After Hackbush cited what he called Thomas’ “rather lengthy criminal record” and his alleged use of “several aliases,” Erie County Judge Shirley Troutman ordered him to remain jailed without bail.

Troutman scheduled pretrial proceedings for Aug. 26 in advance of a possible Dec. 14 jury trial. Thomas’ wife and two other relatives were in court Tuesday but declined to comment after the arraignment.

The investigation into the Dixon slaying was revived after her relatives heard a rumor that the case had been reopened. When they contacted police, they learned that the rumor was false. However, their inquiry prompted the Cold Case Squad to take another look.

Detectives did a DNA analysis of some leftover physical evidence and talked with retired detectives who mentioned that Thomas had been a suspect from the start. The squad then got a DNA sample from Thomas, leading to his indictment.