The alleged victim was only 11 years old at the time and the suspect, David Coffey, was 17 years old.
Coffey, now 53, was arrested Tuesday on kidnapping charges after the victim reached out to police last year and asked them to reopen the case.
The victim told police two men entered her home through a window in the middle of the night and forced her at knifepoint to walk to a home under construction where she was raped and then brought back home.
According to the arrest warrant, Coffey's DNA profile was positively associated with the highest reportable statistic with evidence collected from a rape kit in 1989 -- scientific testing that wasn't available at the time of the incident.
Coffey pleaded not guilty on Wednesday and is being held on $750,000 bail.
Police are investigating whether he was involved with a series of kidnappings and sexual assaults in Danbury during the 1980s.
The second suspect in the case has not been identified, but police released a sketch at that time of who they were looking for in the case.
Anyone with information is asked to contact Det. John Basile at 203-797-4668, the Danbury Police Investigative Services Bureau at 203-797-4662, or the anonymous Tips Line at 203-790-TIPS (8477).
----------
* More Connecticut news
* Send us a news tip
* Download the abc7NY app for breaking news alerts
* Follow us on YouTube