"To the extent that we may have contributed in any way to the public perception that you might have been involved in this crime, I am deeply sorry," Boulder County District Attorney Mary Lacy wrote in a letter to the little girl's father, John Ramsey. "No innocent person should have to endure such an extensive trial in the court of public opinion."
Lacy said newon skin cells that were left behind on JonBenet's long underwear point to an "unexplained third party" and not a member of the family.
"I think the people that are in charge of the investigation are focused on that, and that gives me a lot of comfort," he told KUSA-TV in Denver. He added: "Certainly we are grateful that they acknowledged that we, based on that, certainly could not have been involved."
For years after the slaying, tabloids and crime shows went after the couple, and Lacy's predecessor as district attorney, Alex Hunter, said in 1997 that the parents were under an "umbrella of suspicion." News reports also cast suspicion on JonBenet's older brother, Burke, who was 9 when his sister was killed.
"The only evidence that suggested that they might have had something to do with this crime was the mere fact that they happened to be in the home the night their daughter was bruatally murdered four floors below their bedroom," said L. Lin Wood, an attorney for the Ramsey family, on the CBS News Early Show.
The suspicions outlived JonBenet's mother, Patsy, who died in June 2006 of ovarian cancer at age 49 in Atlanta, where the family moved after JonBenet's death.
"My first thought was obviously I wish Patsy Ramsey was here with us to be able to at least share vindication of her family," said Wood. "There are many people in this country, if not around the world, that also owe John and Patsy Ramsey and Burke Ramsey an apology."
"This is a long time coming," Patsy Ramsey's sister, Paulette Paugh, told CBS affiliate WGCL-TV in Atlanta. "We always knew no one in the family had anything to do with it. It's nice to hear the Boulder County District Attorney's office is finally coming forward with this information... I hope the person who did this is still alive so we can meet him face to face."
"Patsy was a very resilient person, very faithful to her god and she knew in her heart what the truth was," Paugh told CBS News Early Show anchor Maggie Rodriguez. "She went to her maker knowing she had a clear conscience and a full heart."
Early in the investigation, police found male DNA in a drop of blood on JonBenet's underwear and determined it was not from anyone in her family. But Lacy said investigators were unable to say who it came from and whether that person was the killer.
Then, late last year, prosecutors turned over long underwear JonBenet was wearing to the Bode Technology Group near Washington, which looked for "touch DNA," or cells left behind where someone has touched something.
The laboratory found previously undiscovered genetic material on the sides of the girl's long underwear, where an attacker would have grasped the clothing to pull it down, authorities said. The DNA matched the genetic material found earlier.
Lacy said the presence of the same male DNA in three places on the girl's clothing convinced investigators it belonged to JonBenet's killer and had not been left accidentally by an innocent party.
"It is therefore the position of the Boulder District Attorney's Office that this profile belongs to the perpetrator of the homicide," she said in a statement. In her letter to the Ramseys, she said the DNA evidence "has vindicated your family."
She said investigators hope someday to find a DNA match in the ever-expanding national DNA databank.
"This case is going to be solved one day by a random hit on the DNA in the database," family attorney L. Lin Wood told CBS Evening News anchor Katie Couric. "As you know, many cases that have been going on cold cases for years, in fact, are solved years later by a random DNA hit."
Through a spokeswoman, Lacy declined to comment any further.
John Ramsey found his daughter's strangled and bludgeoned body in the basement of the family's home in Boulder on Dec. 26, 1996.
The fact that John and Patsy Ramsey were in the house at the time of the killing fueled speculation that one of them wrote the bizarre three-page note found at the scene. It was written on a pad that came from the house and demanded a ransom that was close to the bonus John Ramsey had received that year: $118,000.
"We should have just stood right up there in the beginning and said, 'Okay, charge me.You think i'm guilty? Charge me, or clear me,'" Ramsey told 48 Hours correspondent Erin Moriarty.
Lacy had previously expressed doubts that the parents were involved. In 2003, a federal judge handling a defamation lawsuit in Atlanta involving the Ramseys said evidence in the case was more consistent with the theory that an intruder killed JonBenet, and Lacy said she agreed.
Less than two months after Patsy Ramsey died, the case appeared to blow wide open with the arrest in Thailand of John Mark Karr, a sometime teacher obsessed with the little girl's slaying. Karr made bizarre, detailed confessions to the killing, but authorities said DNA evidence showed he did not commit the crime.