As parents decide on their children's immunisation, their only concern is whether it is in the child's best interest. Few other decisions in the whole field of immunisation are that pure or that simple. Everywhere else one looks there are financial interests, sometimes obvious, sometimes covert.

When government officials make statements about the absolute safety of the measles, mumps and rubella (MMR) jab they are under pressure from the Treasury to ignore evidence to the contrary. When their advisers say that no more research is needed into MMR's side effects, they may really be saying that companies in which they have an interest don't want to do more expensive research with uncertain consequences.

This is thoroughly unsatisfactory. Childhood immunisation is by far the most cost-effective part of the health service. It provides one third of all the years of added life expectancy that the NHS produces, for one-thousandth of the budget. Overall it is extremely safe but, like every other medical procedure, it can never be 100% safe. MMR is made up of three live viruses and is intended to produce long-term immunity. It would be very surprising if there were not some long-term side effects as well as short-term ones.

If childhood immunisation is such a cheap yet effective part of the NHS, how and why should it be affected by financial considerations? It starts with the bribes offered to GPs -- £2000 or more if a GP immunises at least 90% of the children in the appropriate age range on their list. Ever since that scheme started, we have heard examples of families being taken off GP lists because they refuse MMR .

Sometimes the threat is much nastier than having to change GP. I have heard of two families with long-term foster children being told by social workers that they will never be allowed to adopt the children if they do not let them have MMR.

Next comes the question of side effects. One reason why health officials play down the possibility of any side effects of MMR is that as soon as vaccine safety is in doubt, levels of uptake drop and more children are at risk. Parents will take that risk when most children are immune because the risk of their own child catching any of the three diseases is very low and immunisation is mainly a social duty of preserving 'herd immunity'.

But if immunisation is a social duty, it follows that the state should recompense children damaged in the process. That happens in the United States, where more vaccine damage payments are made after MMR than any other vaccine, and the total payouts are close to $1 billion (£0.7bn). In the UK, on the other hand, we have a mean vaccine damage payment scheme and a Treasury that has no intention of making it fairer.

It is much easier to deny that MMR causes side effects if you don't bother to look for them, hence the complete lack of interest among government officials in trying to replicate Andrew Wakefield's work, which started the present scare. He might just turn out to be right and that would be extremely expensive, goes the logic, so much better to stick with the sort of statement to parliament given by Health Minister Tom Sackville after the mass immunisation campaign in 1994. Having admitted to 530 serious adverse reactions, the minister said: 'All those cases ... with a clear link between the reaction and the vaccine made a complete recovery. For children in whom recovery has been incomplete, the evidence did not support an association with the vaccine.'

It is not only government doctors who do not wish to know. Any evidence of long-term side effects would make it much more difficult for the vaccine manufacturers to defend the class action being brought on behalf of more than 1000 children whose parents believe them to have been seriously damaged. Thus, even now, trials of possible new vaccines are conducted both by industry and government doctors with follow-up of the children involved for as little as three weeks.

The Medical Research Council group, set up to decide what research is needed into the recent tenfold rise in autism rates, unsurprisingly decided that no further research was needed into links between MMR and autism. Three members of the group were doctors acting for the vaccine manufacturers in the legal case.

Doctors may have conflicts of interest that alter the advice they give. This problem has grown rapidly over the past 20 years with changes in the way medical research is funded. There was a time when scientific research was either pure or applied. Pure researchers just wanted to find new knowledge, regardless of whether there was any immediate use for it. Applied scientists looked for ways to use new knowledge for the greater good of mankind. Most research was funded by government.

Now, the majority of medical research is funded by industry, and the driving force has become the commercial interest of the sponsor. Dorothy Nelkin, a leading American sociologist of science, recently said : 'Science is a big business, a costly enterprise commonly financed by corporations and driven by the logic of the market. Entrepreneurial values, economic interests, and the promise of profits are shaping the scientific ethos.'

Sometimes the influence of profit is direct. There have been several examples of researchers deliberately changing research results to favour a drug in which they have a commercial interest. Usually the effect is more insidious. A study of articles in medical journals reviewing the value of a particular group of drugs showed that authors with a financial link to manufacturers of the drugs were much more likely to support their use. In most cases the financial link had not been declared. That is why two dozen prominent scientists and ethicists wrote last week to more than 200 leading medical and scientific journals demanding far more rigorous policies for disclosing authors' financial interests.

In the current debate over MMR, it is insidious influence that is at work. Many government advisers on the Committee on the Safety of Medicines and the Joint Committee on Vaccination and Immunisation have financial links to pharmaceutical and vaccine manufacturers. The latter would not dream of telling the advisers what to say. Nevertheless there will be a clear understanding that advisers who say things against the companies' interests will find, for instance, that the funding for their research assistant will dry up or they are no longer invited to give papers to conferences held in exotic locations.

That would seem to explain why none have recommended using the present research opportunity. Since so many parents are refusing MMR for their children but are willing to have the single measles jab, it would be possible to set up a large-scale, prospective comparison of MMR and measles jabs, with long-term follow-up. It has never been done because previously it was thought unethical. Yet it could provide really useful information to answer many of the present uncertainties, and could now be done ethically.

It won't be done, of course, because it would upset too many vested interests. But if we continue to allow government doctors and advisers to consider only short-term commercial interests, history tells us that we are likely to pay a much higher price in the long term.

Dr Richard Nicholson is the editor of the Bulletin Of Medical Ethics