If this is true, it is dynamite. Doctors and officials in America and Britain have long tried to explain away the increases in autism by claiming that we just had not diagnosed the disease properly before.

It remains to be seen how people react to the new research, but there is no question that it has finally opened up the debate. Dr Robert Byrd, who led the California team, said that it was now important to investigate possible causes of autism, including vaccinations such as the triple mumps, measles and rubella (MMR): “A large number of our families believed vaccines were to blame. Until we can definitively answer that question it seems the research in autism is stuck.”

Will this finally make British officials take autism seriously? Although the Medical Research Council says that the disease now affects one in 166 British children under the age of eight — a tenfold increase since 1988 — the Government has been strangely reluctant to investigate this crippling brain disorder that often leaves children unable to speak, rocking compulsively and unable to form normal social relationships. This is because the Department of Health is terrified of undermining confidence in its vaccination programme. But its dogmatic approach has already lowered confidence in the very vaccines it wants to protect.

Scientists who have dared to suggest that autism and MMR are linked have been treated as heretics — the Prime Minister has accused them of “scare-mongering”.

So far, so medieval. But the Inquisition isn’t working. The more the Government insists that MMR and other vaccines are safe, the more alarm there seems to be.

More than a thousand families are going to court next year claiming that their children have been damaged by the MMR vaccine. Cases are pending from a further 100 who claim that their children have been damaged by the vaccine for diphtheria, pertussis, tetanus (DTP). Vaccination rates for MMR have fallen so low that the Department of Health is predicting a measles epidemic. An ICM poll in July said that only 55 per cent of adults have confidence in the MMR vaccine and that 76 per cent would support an inquiry into whether it is linked to autism.

Scares are created when people sense that they are not being told the whole truth. “Pretty much the first lesson you learn in medical school,” says Dr Richard Nicholson, editor of the Bulletin of Medical Ethics, “is never to use the words ‘never’ or ‘always’. There is no absolute certainty in medicine. The Government is being dishonest by saying MMR is totally safe.”

David Thrower, whose son Oliver deteriorated into autism after receiving first a measles/rubella jab and then the MMR, says: “The Department of Health suspends common sense. The main objective of the department seems to be to preserve public confidence, rather than investigate suspected adverse consequences. People are scared to strike a match in case the whole thing explodes.”

No one has proved a link conclusively between autism and vaccines, but there is a small but growing body of research that raises serious questions. What is strange is the Government’s refusal to take this research seriously.

The first scientist to raise the alarm was Dr Andrew Wakefield, a consultant gastroenterologist at the Royal Free Hospital in London, who published his findings in The Lancet in 1998. He had noticed a huge increase in cases of inflammatory bowel disease since the 1970s and closer examination showed that many of his patients were infected with the measles virus. Astounded by the findings, he investigated and concluded that the measles virus alone was not causing the illness — it was the presence of the mumps virus that made the disease possible. His later research suggested that many children developed autism shortly after receiving the MMR vaccine and that 24 in 25 autistic children he examined had traces of the measles virus in their gut.

The Department of Health went to great lengths to rubbish Dr Wakefield’s research, and officials have insisted that no other study has replicated his work. But in June, Dr Arthur Krigsman, from the New York University School of Medicine, told a US congressional committee that in 90 per cent of his autistic patients he had found a pattern of inflammatory bowel disease identical to that found by Dr Wakefield.

Earlier this year Professor John O’Leary and colleagues in Dublin found the vaccine strain of measles virus in the gut of 12 vaccinated children who had both bowel disease and autism. In August, Professor Vijendra Singh at Utah State University found that autism might be linked to an antibody response to MMR.

Some researchers have suggested that autism may be a new form of mercury poisoning. Studies have found high rates of autism in places where exposure to mercury is high, such as Brick Township in the US and some Japanese cities. Mercury is a neurotoxin that is used as a preservative in some vaccines.

In the US, large payments are being made to children damaged by thiomersal, the mercury preservative used in the US (though not the UK) version of the MMR vaccine. More than $1 billion has been paid out under the National Vaccine Injury Compensation Programme, established in 1986 by US drug companies and the Government.

Around 12 of the 18 vaccine doses that the average American child receives before the age of two contain mercury. Petitioners claim that this adds up to almost 30 times the level considered safe for an adult. In 2000, a study by the American Centres for Disease Control and Prevention suggested that three-month-old babies exposed to 63 micrograms of mercury were two-and-a- half times more likely to develop autism.

Mercury is not used in MMR in Britain, but it is present in some other vaccines. Dr Richard Halvorsen, a London GP, believes that “there is potential for interaction between medical interventions — mercury and MMR may somehow be co-factors in triggering autism. At the moment there is no other sensible explanation for the massive increase in autism.”

Last year the Department of Health asked UK vaccine manufacturers to stop using mercury “where feasible”, but a spokesman said it had set no timetable and will not be monitoring the manufacturers’ response.

Health officials generally seem more interested in discrediting scientists than in investigating whether health is really at risk. Some of the studies cited by the Government in its contention that MMR is safe simply look at the old case notes from the children with autism. They do not examine patients. Most of the research does not compare children who have had MMR with those who have not, nor does it compare children before and after MMR vaccination.

Responding to criticism from the Government’s Public Health Service Laboratory last month, Professor Singh said: “If they enter their same old data in the statistical equation they will continue to find the same old answer, ie, there is no possibility of a connection between MMR and autistic regression. I do not wish to show disrespect towards them, but please do me a favour and ask them what new research they have done to discredit my research. The answer will be none.”

Some of the other studies cited by government have been linked to vaccine manufacturers. A Finnish study which claimed to prove that there was no link between MMR and autism was paid for by Merck, the US vaccine manufacturer. Last month, the Department of Health announced that it had given £300,000 to fund a study that would attempt to copy Dr Wakefield’s research. Campaigners have since discovered that one of the lead members of the team, Dr Phil Minor, is retained by Glaxo-SmithKline, Britain’s biggest MMR manufacturer. Dr Minor was also a member of the Medical Research Council’s review body into autism which concluded last year that there was “no evidence” to support a link. A third of the members of the UK Committee on Safety of Medicines, which has advised that the triple MMR is safe, have declared personal or non-personal links with drug companies that make the vaccine.

Dr Richard Nicholson, of the Bulletin of Medical Ethics, says that the Government prefers scientists who have already made up their minds. “If you’ve got people funded by government who for years have been shouting from the rooftops to anybody who will listen that there is no link between MMR and autism, how much credence do you give the results? Why does the Government think it is worth spending money on this kind of research unless it wants it for propaganda purposes?” Lord Clement-Jones, Liberal Democrat spokesman in the House of Lords and vice-chair of the All-Party Parliamentary Group on Autism, feels similarly frustrated. “The argument has got extremely theological,” he says, “and has gone well beyond the point where people are discussing the facts.”

The Government has had a long time to get to grips with these issues and to prevent the slide into emotion. In the mid-1990s, two men raised their own concerns privately with the Department of Health about MMR in the hope that the Department would investigate and prevent a health scare. One was Dr Andrew Wakefield, who was subsequently rubbished by government and accused of being a selfpublicist.

The other was Richard Barr, a partner in one of the law firms that is co-ordinating the claims of more than a thousand families who believe their children have developed autism as a result of receiving MMR.

“In 1996,” says Barr in a recent letter to The Lancet, “I became so concerned about what seemed to be happening that I wrote to the chairman of the Committee on Safety of Medicines offering to make available the medical records and other information about children who had apparently been affected by the vaccine. My offer was put to the Government on three occasions but was turned down.” It is not clear why the Department of Health was so reluctant to investigate. But under pressure, officials eventually made a small concession. They agreed to send questionnaires to Barr’s list of parents about their children’s symptoms, although it is not clear how they expected this to shed any new light on the matter.

Richard Barr again: “The Department of Health, without referring to us or our clients, set up a working party to look at the families’ questionnaires, and questionnaires they later sent to the treating family physicians. They now use the resulting report as part of the evidence to support the assertion that the MMR vaccine and autism are not linked. They describe it as involving a detailed assessment of more than 100 children’s records referred to them by solicitors, yet the report itself states that it took into account only evidence derived from the parental and medical questionnaires. The report’s conclusion is that it is impossible to prove or refute the suggested associations between MMR vaccine and autism, pervasive development disorder, or inflammatory bowel disease because of the nature of the information used.”

The Department of Health’s intransigence on MMR, and its apparent nonchalance about links with drug companies, is not only undermining confidence in the MMR vaccine but leading some parents and doctors to question the whole childhood vaccination programme.

“We need to take stock,” says London GP Dr Richard Halvorsen. “We’re introducing more and more vaccines earlier, and that concerns me. When do we get to the stage where we could be giving too many? I believe that any medical intervention has the potential for side- effects in some people. We have to be pretty damn sure that we are doing more good than harm.”

Grandparents who had only one jab in childhood — against smallpox — are amazed that their grandchildren are routinely receiving 22 vaccine doses before they are old enough to start school. British babies now receive six vaccine doses in one go at the age of eight weeks, including DTP. Britain has had the most aggressive DTP programme in Europe since 1990, when the programme was accelerated to reduce “drop-out” rates. At the same time GPs were given extra money if they managed to achieve 70 per cent or 90 per cent vaccination coverage. With this incentive, the proportion of GPs reaching the highest coverage level went from 60 per cent to 90 per cent in two years.

Britain’s childhood vaccination programme is clearly convenient and profitable for both drug companies and GPs. But is it sensible? Allison Edwards does not think so. Her son Jonathan was born a week and a half early but still had his first set of injections at eight weeks because “they don’t count for early births, they just start at week one. I asked questions and was made to feel like a troublemaker. The health visitor was push, push, push. Nothing checked — no questions about possible contraindications — they just went straight in there with the needle. I think his little body couldn’t take it.”

Jonathan Edwards, now 5, is diagnosed as autistic, with a mental age of 12 months.

The astonishing thing about many of the parents who believe their children have been affected by vaccines is how moderate they are. Most seem bewildered by the Government’s lack of interest, rather than bitter. Most support the overall vaccination programme. David Thrower again: “We must protect children from communicable diseases. But we need to screen out a small percentage of children from the immunisation programme to protect its credibility for the future.”

This measured approach is in stark contrast to the Government’s tactics. Fear of MMR has led many parents to travel around the country to pay for single doses. The Government has responded by restricting imports of the single doses, which is further reducing the number of vaccinated children. Parents are taking matters into their own hands and are trying to assess the relative risks of vaccination for themselves. If vaccination rates fall too much farther, a new generation of children could be in danger from serious diseases, such as measles.

Something must be done before next October, when the MMR cases will come before the High Court.

“If the legal judgment goes against the vaccine manufacturers,” says Dr Richard Halvorsen, “I fear the public confidence in the whole immunisation policy may come crashing down.”