Sir Alec Jeffreys, who invented DNA fingerprinting, said a match did not necessarily demonstrate a person's guilt or innocence.
It follows claims that DNA samples matched to Madeleine had been found in her parents' hire car and holiday apartment. Sources said the traces were being treated by Portuguese detectives as strong evidence that Madeleine's body was placed in the car.
However, Sir Alec told BBC's Newsnight programme: "There are no genetic characters in Madeleine that are not found in at least one other member of the family.
"So then you have an incomplete DNA profile that could raise a potential problem in assigning a profile to Madeleine given that all other members of that family would have been in that car."
Sir Alec, 57, added: "DNA testing seeks to establish whether DNA sample A from a crime scene came or did not come from individual B.
"So if you get a match there's very strong evidence that it did come from B. It is then up to investigators, the courts and all the rest of it to work out whether that connection is relevant or not.
"So DNA doesn't have the words innocence or guilt in it - that is a legal concept. What it seeks to establish is connections and identifications."
Off-camera, Sir Alec said he was prepared to act as a witness for the McCanns.
His caution came as a leading genetics expert also called into question the value of DNA evidence in its own right. Dr Paul Debenham, a member of the advisory body the Human Genetics Commission, said there could be legitimate reasons as to how DNA from Madeleine found its way into the hire car.
Prosecutors would need to establish that it got there as part of a criminal process and not through chance contact, he said.
Dr Debenham said: "With the current highly sensitive DNA methodologies we can deposit DNA as a trace amount just from contact with a fabric. And that fabric can touch another surface where the DNA is passed on.
"So there is a situation where there is a legitimate or a possible explanation as to how the DNA got on the back seat despite the individual not being there, but through some legitimate transfer of garments, clothes or soft toy.
"It questions the value of that particular evidence in interpreting what happened."
I have already made the comment that I think that this is the Azaria/Lindy Chamberlain case redux, because I see a similar turn in the course of events. The Portuguese police seem to be of the opinion that they need to get a resolution on this case, and they have started pursuing a course of action that is based upon the flimsiest of evidence. In the Chamberlain case, the prosecution built up their case against Lindy Chamberlain based a work up by a forensic laboratory technician who identified what turned out to be sound deadener and coca cola stains as traces of blood belonging to Azaria. Based upon this forensic testing result, Lindy was charged with murdering her baby by slitting the child's throat, even though Azaria's body was not found. Madeleine McCann is classified as a missing child. Her body has not been found, yet the Portuguese police have come to the conclusion that Kate McCann must have overdosed her child with a sedative, hidden the body for almost a month and then Gerry McCann disposed of the body. These conclusions are based upon DNA samples in a car that the McCanns hired after Maddie had disappeared. There is a claim that specks of blood were found in the car and that this blood belonged to Maddie. If Maddie was dead for so long prior to be "dumped" then surely it would not be possible for her blood to be found in that car for obvious reasons. The real experts have cast doubt upon the DNA findings for other reasons, so at least I could be on the right track in thinking that there is something very wrong with the way in which the Portuguese police are handling the investigation.
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