At 3pm today St Paul's Cathedral will fall silent as more than 200 parents of children with autism gather for a service of prayer. Among them will be Ivan and Charika Corea, whose five-year-old son, Charin, has suffered from the condition for more than three of his five years.

Many others in the congregation will be wondering the same thing as Ivan and Charika. Did their faith in a government policy of inoculation against measles, mumps and rubella lead to the autism now suffered by their children?

'At 18 months Charin was animated and about to talk,' Ivan said. 'He had the MMR vaccine a few months earlier. By 24 months he had turned inwards: no speech, no eye contact. He was in a world of his own, like a different child.'

The past week has been the turning point for the MMR controversy stalking the Government. A measles outbreak, more scientific research and poll after poll revealing public disquiet over the vaccination has again put the issue of children's health at the centre of political and scientific debate.

Downing Street and the Department of Health insist this is just a thin concoction of coincidences whipped by the media into a frenzy that is scaring the country witless. Its roots go deeper, however, involving the public attitude to science and medical advice to trust in the Government.

It is also the story of how easily fear takes flight: how a few pages in a medical journal, written by a team of doctors - who admitted that 'we did not prove an association between MMR vaccine and the syndrome described' - could lead four years later to nationwide panic, the bitterest of political rows and a revolt against the medical establishment that could yet lead to the deaths of children. Its genesis goes back more than a decade.

On a warm autumn morning in 1988 a group of nursery age children gathered at the Queen Elizabeth II Conference Centre in central London for a special event. As they munched apples and bananas and the floor beneath them became covered in discarded peel, Edwina Currie, the Tory Health Minister, walked to the rostrum to announce one of the most important changes in child health policy for a decade. The triple vaccine, MMR, would be offered to parents.

Scientists had been warning the Department of Health for more than a year that the measles epidemics periodically sweeping the country could only get worse. In some years in the Eighties more than 80,000 children caught the disease, more than 100 of them died and thousands were left with damaged hearing and eyesight.

The single measles vaccination used then simply was not working, with take-up rates too low to create the crucial 'herd immunity'. How could take-up rates be increased? The Joint Committee on Vaccination and Immunisation said allowing children to have more than one inoculation per jab would increase participation. Parents would not have to make multiple journeys to clinics. Currie agreed.

In 1987, 11,000 families took part in trials of MMR, used around the world with no apparent ill-effects and no hint of a link with autism.

Take-up of MMR was rapid, as parents clamoured to protect their children against a nasty disease. By 1 December 1988 a million doses had been dispatched. Measles outbreaks tumbled. Questions were asked in Parliament about why older children could not have MMR. The last death from measles was in 1992. The Government was relieved: the triple vaccine had worked.

Reel after reel, hour after hour, the stacks of home-made video tapes kept carefully in boxes in the office of a Cheshire solicitor tell the same heartbreaking tale. Made by dozens of families, they show a procession of babies and toddlers laughing, crawling, playing. They are remarkable for only one thing: they represent a way of life now lost.

The home videos belong to some of the 1,000 families preparing to go to court over what they believe is damage caused by the MMR jab. Until the medical establishment can explain to these parents what really causes autism, nothing will convince them that it is not the injections.

Eleven years ago, the mother of a baby who had suffered mild meningitis after having the jab in 1990 asked a Norfolk solicitor, Richard Barr, for advice. She was the first of a growing queue of parents approaching Barr about what they believed were vaccine-damaged children. Was MMR totally safe?

Simultaneously at the Royal Free Hospital in London, Andrew Wakefield, a specialist in bowel disorders, began receiving an oddly similar series of calls from anxious parents. The one thing they had in common was that their children, apart from having inflammations of the gut, were autistic.

By 1995 Wakefield had amassed enough cases to tell the doctors' magazine Pulse he believed there was a connection between autism and MMR. It was the first ripple of a coming tidal wave.

Five months after the 1997 election, the new Public Health Minister Tessa Jowell met a deputation that marked a significant step forward for the anti-MMR campaign. The Labour MP Llew Smith, Barr, Wakefield, and a Cheshire mother called Jackie Fletcher, who set up the pressure group Jabs to campaign over vaccine damage after her son Robert was diagnosed as an epileptic, filed in for what was meant to be a strictly private meeting.

They had come to warn the Government of a bombshell: Wakefield was completing a paper for another medical journal, the Lancet, which he believed proved a link between MMR and autism.

Flanked by the Government's chief medical officer, Sir Kenneth Calman, Jowell agreed that once Wakefield had published it, a conference of experts would review the evidence. The two sides parted amicably.

It was February 1998 when Wakefield finally told a press conference at the Royal Free his study of 12 children with an unusual bowel syndrome had discovered traces of the measles virus in their guts. His working hypothesis was that the MMR jab might have damaged their immune systems, letting the virus take hold and leading somehow to the development of autism in some of the group.

For him it was a 'moral issue': the triple jab should be suspended, he said.

Arie Zuckerman, dean of the Royal Free's medical school, interrupted to say he did not believe the evidence warranted stopping the jabs. It was too late: headlines the next day warned of a 'new child vaccine danger'.

Within a month, Jowell organised the promised summit at the Royal College of Surgeons, involving 37 experts. According to confidential minutes seen by The Observer, several conceded that parents might think there was a connection because the MMR jab was given when the first signs of any autism usually become obvious. But, it was pointed out, studies of men with brain tumours had shown their wives regularly remembered head injuries they believed must have caused the growths, even though cancer is not caused by blows to the head. There was a 'basic human tendency to ascribe blame to a specific incident or event', but 'no evidence to indicate a causal link between MMR vaccination and autism', the minutes said.

Outvoted by dozens of his peers, Wakefield could only ask for the minutes to note that he disagreed. The next day Calman issued a categorical statement that MMR was safe, but that more research was needed into autism.

Those words have echoed down the years, as doctors in Sweden, the US and Finland tried and failed to confirm Wakefield's results. Paediatricians at his own hospital studied nearly 500 children in 1999 and found no increased risk of autism after the jab.

And while autism cases are rising, there was no sudden jump after 1988 when the vaccine was introduced, suggesting that better diagnosis rather than the jab is the cause. In California, researchers discovered diagnoses of autism shot up in the late Eighties, though the vaccine had been around for 15 years by then. Wakefield's findings were buried under a tidal wave of rejection from the global medical establishment. Yet the scare persisted.

'Parents don't think about whether their child is at a 1 per cent risk of an adverse reaction, or a 2 per cent risk,' Currie said last week. 'For every parent, the risk to their child is 100 per cent.'

When early last year the Department of Health commissioned yet another review from the Medical Research Council on the causes of autism, it was quietly confident the result would be the same as that of every other major study since: there was just no evidence for Wakefield's theory.

It did. But by the time the report thudded onto medical journalists' desks last December, the row had taken a sharp new twist: Wakefield had been forced out of his job at the Royal Free by colleagues whose patience had finally run out. The movement had its first martyr.

Soon it also had its first serious ethical dilemma: Tony Blair found himself asked repeatedly whether his son Leo had had the jab, and he refused to say. Did one baby's right to privacy really outweigh the dangers to thousands of children if public confidence in MMR collapsed?

The row rumbled on, with the Government convinced as Christmas turned into the New Year that the debate would lessen and vaccination rates would rise again.

Then came what everybody had feared. Ten days ago in the heart of south London's 'nappy valley' - a middle class enclave of families with young children - an outbreak of measles emerged. There are a few dozen such cases every year, but this time the atmosphere was politically charged.

Liam Fox, the Shadow Health Secretary, immediately called for the Government to consider making single vaccines available in areas of low uptake.

Fox had floated the idea before but this time it coincided with a poll showing most parents now thought the Government should offer a choice. By Wednesday, measles had erupted in a Gateshead school, and Fox again demanded single jabs.

More damagingly, the Sun claimed last Wednesday that Blair had ordered a review of the cost of single vaccines, suggesting he was wavering. Alastair Campbell, Blair's director of strategic communications, insisted it was untrue. Blair had not even asked for information on the issue, although Number 10 was preparing a dossier of evidence against any link between MMR and autism to be released later in the week.

Despite the denials, the public saw another chink in the triple vaccination armour. On the morning of the Sun story, Blair's health policy adviser, Simon Stevens, set out from Downing Street for a meeting in Alan Milburn's office. With the Health Secretary were Yvette Cooper, the Public Health Minister, who has just returned from maternity leave, and the Government's Chief Medical Officer, Professor Liam Donaldson.

All four were infuriated by the front-page story in that day's Daily Mail, citing a study by the Dublin virologist Professor John O'Leary showing the presence of measles virus in gut tissue as fresh evidence that MMR might be dangerous. Yet O'Leary made it clear he did not know if the children he studied had had the vaccine.

The four agreed it was time for the weapon of last resort: Donaldson, who - as a doctor rather than a politician - has most credibility. A press conference was hastily booked for the next day.

There, Donaldson warned that parents rejecting MMR were playing 'Russian roulette' with children's lives. He has a gift for colourful phrases, but the words were heartfelt: he has told friends he would not stand for a change in policy, and is 'passionately' for MMR.

Nobody, however, believes the scare is over. Ministers are working on a new advertising campaign to shore up vaccination rates. The issue is overshadowed by the whooping cough experience in the Seventies, when a fall in vaccinations after a health scare led to the deaths of 51 children.

At the London School of Hygiene and Tropical Medicine, specialists are combing the medical records of more than two million Britons for evidence of the causes of autism in the biggest study yet. Scientists increasingly believe a complex genetic trigger is to blame, but that could take years to unravel.

Meanwhile Wakefield is now studying the impact on children not just of the first MMR jab but of the booster given before they are five. Without this, a child has only 90 per cent protection. And the parents of the vaccine-damaged children come to court next October, another potential flashpoint.

On one point both warring sides agree: the uncertainty cannot go on.'[The parents] want a conclusion, and the constant bickering does not help,' said one source close to the families.

'Everybody forgets that these children who, according to their parents, were totally normal. Now they're will need care for the rest of their lives.'