No public health issue of recent years has attracted such heated debate as the question of whether the MMR vaccine can cause autism. The MMR jab combines three childhood vaccines, against measles, mumps and rubella, into one injection, which is first given to children at around 12-18 months. It has virtually eradicated these diseases from the UK, and throughout the world it has saved hundreds of lives.

Recent years, however, have seen the rates of MMR vaccination decline. In some areas of the UK, only 60% of children are receiving MMR. This decline has already let to a rise in the number of measles infections, and there are fears of an epidemic outbreak.

The reason for all the concern over MMR is the suggestion that the vaccine might in fact be damaging some of the children it was supposed to protect.

Rosemary Kessick's 16-year-old son William is severely autistic. Shortly after William had his MMR shot, Rosemary noticed a change in his behaviour. He also started suffering from recurring bowel problems. Convinced the three things were connected, she took William to the Royal Free Hospital in north London to see Dr Andrew Wakefield, a specialist in bowel diseases.

Wakefield became convinced that William and a number of other children he had examined were suffering from a new kind of bowel disease that could be linked to their autism. What's more, he started to wonder whether this condition was being caused by the MMR vaccine. At the press conference to coincide with the publication of this research he suggested that the combined MMR jab should not be used. The result was a media storm.

Ever since, scientists have been looking at the evidence to see whether there really is a link between autism and the vaccine. The medical community has relied mainly on epidemiology - the statistical study of large populations. These studies have overwhelmingly found no link between autism and MMR. Opponents claim that some of these studies might have flaws, but there are over a dozen epidemiological studies in different countries that use different techniques that have reached the same conclusion. At the very least, these studies show that the large increases in rates of autism that have been reported in many countries around the world cannot be due to MMR.

However, the opponents of the vaccine point out that epidemiology can't rule out an increased risk to a small number of children - a vulnerable subset. They pointed to distinctive features of some of the autistic children that they said was evidence of a possible connection with MMR. Firstly, these children seemed to have a novel bowel disease that was unique to children with autism; and in 2002 Wakefield, working with virologist Prof John O'Leary, claimed to have found the measles virus inside tissue samples from autistic children.

Since then, debate has raged over these claims. Little independent clinical research into these claims has been funded - to the anger of many parents. But now at last the deadlock is being broken.

Timothy Buie is a paediatric gastroenterologist in Boston. What makes him unique is that he works in a clinic that specialises in the care of children with autism and related disorders. Like Dr Wakefield, he has found that many of these children do have real bowel problems that are worthy of investigation.

But despite having performed colonoscopies on hundreds of children, both with and without autism, Dr Buie has so far seen nothing that convinces him the autistic children have a new or distinctive form of bowel disease. His research is still ongoing, but it casts doubt on one aspect of the Wakefield hypothesis.

But perhaps the most crucial question is whether the measles virus really is persisting in the bodies of autistic children; and now that question too has been investigated. A new, unpublished study has examined blood samples from a group of 100 autistic children and 200 children without autism. These samples have been examined using the most sensitive methods available. They found 99% of the samples contained no trace of the measles virus, and the samples that did contain the virus were just as likely to be from non-autistic children. The study therefore found no evidence of any link between MMR and autism.

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