Officially, the triple MMR vaccine is safe. Thousands have their doubts ­ including the Vallely family, who have particular reason to fear its alleged harmful side-effects. But what really scared them was the obfuscation they encountered when they sought a more traditional alternative

It was somewhere around Scunthorpe that I realised what a hell of a long way it is to Louth. When you eventually get there ­ after a three-hour drive, in our case ­ it's a pretty, little market town. But a long way from everywhere. Unless you live there, of course. In which case, it's everywhere else that's a hell of a long way off. It all depends on your perspective.

We had gone there two months ago with our 16-month-old son, Thomas, to consult Dr Peter Mansfield, the GP who next week appears before the General Medical Council's Interim Orders Committee ­ its new, fast-track disciplinary body, introduced to cope with grave challenges to public confidence in doctors by cases such as that of the murderous GP Harold Shipman. Yet it is to be convened next Wednesday for far more dubious reasons.

Dr Mansfield is arraigned before the committee at the insistence of Professor Brian McCloskey, the director of public health in Worcestershire, who has accused the GP of putting children "at risk" through actions that are "at variance with normal clinical practice". The heinous offence that has provoked this? Dr Mansfield is offering measles, mumps and rubella vaccinations in single doses, instead of the government-approved three-in-one MMR jab. For this, the GMC committee could ban Dr Mansfield from practising.

It was a long journey that had brought us to this place. In more ways than one. Some six years ago my wife, Christine Morgan, made the original File on Four documentary on BBC Radio 4 that first reported fears among a growing group of parents ­ now numbering 1,800 families ­ that the MMR vaccine was to blame for the autism that had struck down their children. They told frightening stories of how the MMR jab had been followed by fever, fits and a night of screaming, after which their bright and lively child had become unrecognisably uncommunicative or violent in the first signs of a disintegrative psychosis. For years, senior advisers at the Department of Health pooh-poohed the idea that the two were linked. It was, they said, merely a sad coincidence that autism set in just at the time that the MMR jab was given. There had been a seven-fold increase in the worldwide incidence of reported autism since the MMR was introduced in 1988, but the two events were completely unrelated.

What set new alarm bells ringing was research by Dr Andrew Wakefield, a gastro-enterologist at the Royal Free Hospital in London, who in The Lancet in 1998 claimed that he had found the measles virus in the bowels of children who, after having the triple vaccine, had developed a new kind of autism, or a serious bowel condition called Crohn's Disease. Perhaps the MMR was the cause, he suggested. Other experts castigated his research. The government insisted that the MMR was entirely safe. For me, the issue was an interesting scientific disagreement, which I followed over the years with half an eye. But then our son was born.

The US general Norman Schwarzkopf was, in pep talks to his troops during the Gulf War, fond of using a parable about a pig and a hen discussing a bacon-and-egg breakfast. The hen, he concluded, was involved, but the pig was committed. Suddenly, I felt more than involved in the MMR controversy.

Taking advantage of the access that journalists have to ministers, I buttonholed Tessa Jowell, then the health minister, over tea at the Labour Party conference and asked why concerned parents couldn't opt for the vaccine in the single jabs. These were not safe, she replied; they put children at extra risk. But these were the same vaccines that had been routinely used in the government's official vaccination programme between 1967 and 1988, I said. Well, that was the expert advice now, she said. She couldn't remember why, but promised she would have the research mailed to me. It never arrived. But then, ministers are busy people. There were obviously more important things on her to-do list. But the time soon arrived when there was nothing more important on mine. It all depends on your perspective.

When Thomas was 14 months old, something did arrive in the post. It was the reminder from the local health authority that it was time for the baby's MMR. We went to see our excellent family doctor and aired our concerns. Our GP tried to reassure us, repeating the medical consensus. She was happy to give it to her own child, who was a similar age. She gave us the Department of Health's official leaflets and its website address. We looked up everything on it.

But in the end, despite the faith we have in our GP, we were still worried that if, in a few rare cases, children with highly-sensitised immune systems might react to the vaccine, as the Wakefield research suggested, Thomas could be one of them. His aunt has chronic Crohn's disease. His cousin had such a bad reaction to his first MMR jab that they had to admit him to hospital to do the second. And in the first months of his life, Thomas has exhibited a spectacular series of allergic reactions to a wide variety of things ­ colourings, flavourings, additives and even milk and eggs. We knew that the MMR vaccine is cultivated in chick embryos, and that researchers in Virginia had asserted a link between food sensitivities and autism following the MMR. There seemed no sense in taking the risk with our baby.

All the doctors we knew thought that we were being alarmist. Friends who were GPs, a next-door neighbour who was a paediatrician, my sister-in-law who is a senior paediatric consultant, all told us ­ with varying degrees of frankness ­ that we were being irrational.

There had been, they said, an authoritative English study of 400 autistic children which was the foundation of the Department of Health's claim that the MMR vaccine does not cause autism. But, we replied, that study only monitored kids for a maximum of six weeks after the jab, when more serious signs of conditions affecting the nervous system would not yet have manifested themselves. More research had been done in Southampton, they said. But Christine had been to see the researchers there, and their study wasn't as conclusive as our doctor friends claimed.

Well, they said, there had been a definitive study in Sweden. But there were no children under two in that study, so how could we be sure it was safe for a 15-month-old? There was a study in Finland, too. Yes, but doubts had been cast on its methodology, because it relied on passive surveillance, which critics said missed as much as 80 per cent of cases. To cap it all, the European Union has now announced a £2.5m three-year review of adverse effects following the MMR, and in Washington a Congressional Committee has launched an investigation into the controversy.

What all this added up to was that the research showed that the MMR was safe in an overwhelming number of cases. But it did not reassure us that there was no link in a rare number of cases. So why not opt for single jabs, if they were available?

We scoured the internet to find out where. We knew that a survey in the GPs' magazine, Pulse, had recently shown that only 53 per cent of doctors felt that the government had adequately proved there was no link between the MMR and autism, and 15 per cent said they would be prepared to flout Medicines Control Agency rules and administer single vaccines, if parents obtained them. But the internet produced only a handful of doctors prepared to obtain the single doses. They were in London, Edinburgh, Oxford, Colchester, Worcester and Louth. We took soundings from JABS, a support group for parents of vaccine-damaged children, and decided upon Dr Mansfield. We travelled to Louth to meet him.

"I am not an expert on the MMR," the 58-year-old GP said, as soon as he greeted us in his small surgery on the outskirts of the Lincolnshire town. "I offer no view on whether or not it is safe. But the parents who seek me out have already made the decision not to have the MMR. Nowhere in nature does the human body ever have to cope with three systemic viruses at once. So it is, on first scientific principles, perfectly reasonable for parents to ask for separate vaccines." After an hour's consultation, we felt confident in him – and in the sources of his vaccines – and asked him to administer the single rubella jab there and then. We made an appointment for Thomas to have his measles jab six weeks later.

Before that could happen, the row broke out, with the Worcester Health Authority reporting Dr Mansfield to the GMC over his twice-monthly visits to the city to offer separate-dose vaccination at a clinic set up by concerned parents there.

The response of the senior medical establishment was instructive. It was clothed in the same tone of patronising over-confidence that has characterised its response ever since it withdrew the licence for the single mumps and measles vaccines in 1998, to try to force parents to have the MMR. But what was most alarming was the amount of inaccurate information that was peddled to support the Government's case. The head of the Worcestershire Health Authority displayed a complete lack of knowledge of Mansfield's approach, accusing him of leaving children unvaccinated against German measles for a year after the measles jab – when in fact, the rubella vaccine is the first one that the Louth GP gives. It was only the first of a succession of untruths.

A procession of medical mandarins were trotted out. The quality of single vaccines was less effective, they said – despite the fact that it is the same vaccine, made by the same companies, as in the MMR. Children would be left unprotected for a year between each of the three jabs, they said – despite the fact that they are given at six-week intervals. Children would need six jabs instead of two, they said – despite evidence that vaccines take more effectively in single doses, and that sero-conversion testing shows that a booster is often unnecessary. Time after time, these so-called experts demonstrated to us that they were either ignorant of the facts, or chose wilfully to misrepresent them.

Why? The medical establishment clearly fears that allowing single vaccines will only further undermine public confidence in the MMR – on which uptake is now down by 12 per cent. Why else would the Government respond to parental disquiet with a preposterous £3m advertising campaign for the MMR, which likens those who question the triple vaccine to parents who would abandon their defenceless baby in the jungle in the path of a menacing tiger?

The irony is that – in a post-BSE society where scientific authority is no longer unquestioningly accepted – their attitude is promoting the very scare they purport to be so keen on avoiding. Sceptics may also wonder if they are alarmed by the increasing number of single-vaccine children – there are now around 2,000 – who will constitute a significant control group whose future health can be contrasted with the MMR population.

Thomas is due for his measles jab on Tuesday, the day before Dr Mansfield appears before the GMC. If, for any reason, he were not able to administer it, the alternative for us would not be the MMR, but a trip to France or the United States, where the vaccines are available singly, and where governments do not resort to such bullying tactics.

For those without the resources to pursue such alternatives, the story might end very differently. For the key fact that the health establishment doesn't seem to have grasped – but which Dr Mansfield and a handful of other doctors have understood – is that, for an increasing number of parents, the choice is not between the MMR and single vaccines. It is the single vaccines or nothing.