A cross-dressing Orthodox Jew yesterday pleaded not guilty to beating his elderly roommate to death in Brooklyn, while authorities performed forensic tests on the baseball bat they believe to be the murder weapon.

Howard Goldstein, 56, who once enjoyed wearing wigs, heels and lipstick, appeared in court yesterday in a yarmulke, white T-shirt, khaki pants and canvas sneakers.

He pleaded not guilty to second-degree murder and other charges, including criminal possession of a weapon – “the item which we believe was used to kill [75-year-old Rahamin “Raymond” Sultan], which is a baseball bat,” one law-enforcement source said.

Goldstein’s lawyer, Jay Cohen – who came to court with a book on cross-dressing in his briefcase – plans to launch a psychiatric defense on Goldstein’s behalf.

Goldstein, a Vietnam vet who collected disability checks but sometimes worked as a handyman, is accused of beating Sultan to death in a rent dispute at the pair’s Midwood apartment.

After a friend reported Sultan missing, police went to the apartment. Goldstein opened the door to cops in high heels, makeup and lipstick – and they picked up on a strong odor emanating from inside.

Officers found the elderly victim’s body wrapped in bedclothes, towels and a plastic garbage bag in the living room. Blood was on the floors and walls. Sultan had died as a result of blunt trauma to the head, authorities said.