Brian Kelly - who served four years in jail - has had his case referred to the Court of Appeal in a move that could lead to dozens of similar convictions for sexual assault being overturned.
Kelly was the first person in Scotland to be successfully prosecuted on the basis of DNA evidence and was jailed for six years in 1989.
But two separate studies have concluded that the way the first DNA test was carried out risked producing a ‘false positive’ result because a sample taken from Kelly may have got into a sample of the rapist’s semen found on the woman’s nightdress.
The Scottish Criminal Cases Review Commission (SCCRC) said Kelly’s case could open the door to further appeals by people convicted on the strength of the same DNA test, which was used until 1994.
Kelly’s lawyer, Campbell Normand, said: "Essentially what we are saying is that the expert evidence now available shows that testing procedures carried out on behalf of the Crown were such as to cast doubt on the results they produced in evidence at the original trial.
"That doubt was never put to the jury. It was put to the jury as a fact, which wasn’t actually supported by the scientific evidence. Cross contamination of the samples is the major issue."
The woman, a single mother, was raped at night in 1987 while she was in bed at her Ayrshire home by a man who got in through a window.
In July of that year Kelly, a traffic officer who lived in Largs at the time, agreed to give a sample of his hair and blood believing this would eliminate him from the inquiry.
But two-and-a-half years later he found himself convicted by a majority verdict of raping the woman, largely on the strength of the DNA test.
The decision came despite the fact the woman did not identify him as the rapist even though she knew him. Also on the night in question, Kelly had been out drinking, but the victim did not say her attacker smelled of alcohol.
In 1991 the first doubts began to surface about the accuracy of DNA tests and a study in the United States later found that errors were made in around one in 50 cases.
Two years later Kelly was a free man but his release on parole was delayed because he refused to admit his guilt. He moved to Kilmarnock where he has since worked in a pub and as a lorry driver.
In 1994, the concerns over the system of DNA testing resulted in a major overhaul of the way profiling was carried out.
Kelly continued to protest he was an innocent man and the case was referred to the SCCRC after an attempt to appeal failed to overturn his conviction.
The commission formally referred the case back to the High Court in December 2000 and a hearing is expected early next year.
Robin Johnston, the senior legal officer at the SCCRC who dealt with the case, said if Kelly’s conviction was overturned it could result in legal challenges from others jailed on the strength of DNA evidence before 1994.
"To my knowledge we’ve only referred one case to the High Court based on DNA issues and that’s Brian Kelly’s," he said.
"It could certainly lead to more cases depending on what the view of the High Court is. My understanding is it’s a matter of some controversy and you’re not going to find a uniform view from the scientists."
The decision to send the case back to the High Court was taken after the defence submitted a report by the US-based forensic scientist Dr Simon Ford, which highlighted the scientific concerns over the test.
The SCCRC then obtained a second opinion from world-famous expert Dr Adrian Linacre, of Strathclyde University.
He said there was a possibility that a sample of Kelly’s DNA was mixed with DNA taken from semen on the rape victim’s nightdress during the testing.
"When you look at the gel image in this case there’s a great big, very intense band from the blood sample from Kelly, but a very faint band from the nightdress," he said.
"The issue was whether you had a sample like this producing weak bands that obviously would match because of some of Kelly’s sample had got into the sample from the nightdress. Maybe that’s the reason why we have found bands on the crime scene samples but much brighter bands on Kelly’s sample."
Legal expert Professor Robert Black, of Edinburgh University, said that the ramifications of the Kelly case could be far-reaching.
"It is obviously important because DNA is regarded as crucial so if a doubt is going to be cast upon it, that’s a major, major thing," he said.
"It could mean that other people who were convicted under the old technique will raise this issue."
Leading QC Donald Findlay, who was previously involved in the case and believes it may well have been a miscarriage of justice, said: "I did feel very, very uneasy about it. The DNA was the problem.
"I defended a number of cases on the basis that you really couldn’t trust DNA testing because it was in its infancy.
"But it seems to be pretty impressive nowadays. I’ve had it checked in a number of cases independently and I have not come up with a case to say it’s wrong."