Leroy Johnson Jr., 39, is accused of forcing his way into the women's home and attacking them at knifepoint on November 18, 1996.
Both were blindfolded and unable to identify their attacker. However, Johnson was arrested and charged after cold-case investigators said DNA tests tied him to the crime.
Jurors in the trial in state Supreme Court in Manhattan will not be told of Johnson's conviction for raping McGillis, by law, because the crime occurred more than 10 years ago.
Johnson was 15 when, authorities said, he ambushed McGillis, then an aspiring actress and student, in her Greenwich Village apartment and at knifepoint with an accomplice attacked her and her roommate.
McGillis was able to identify her attacker from police mug shots, and he was later apprehended through fingerprint evidence.
After his conviction, Johnson was sent to a state juvenile facility, from which he escaped. He later served time in prison, was released in 1991 but returned to prison in an unrelated case two years later.
Other details of Johnson's past were not immediately available.
McGillis went on to speak publicly about her attack. In an interview she gave while filming the movie "The Accused," in which she played a hard-nosed district attorney prosecuting an accused rapist, McGillis said she wanted the role because she had first-hand experience of being a rape victim.
Defense attorney Bryan Konoski argued in his opening statement that the DNA samples obtained from the two women had been tampered with and were "not pure."
One of the victims, now 31, took the stand and wept as she recalled details of the attack, and how her attacker said repeatedly, "Bitch, I'll kill you."