Few subjects polarise opinion like vaccination. Since Edward Jenner pioneered the concept more than 200 years ago, it has transformed public health across the globe and vies with antibiotics and anaesthesia as the most significant advance in modern medicine. But, as the recent furore over the cervical cancer vaccine has proven, it is also one of the most controversial.

A 14-year-old schoolgirl, Natalie Morton, collapsed and died within hours of receiving the Cervarix vaccine, fuelling the embers of parental concern and encouraging the conspiracy theorists who populate so many internet forums. That she now appears to have died from an underlying cancer, rather than from a reaction to the vaccine, seems to have been largely ignored. The damage has been done.

I spent yesterday reading through some of the posts on the Times’ website, and surfing the net, and there are a number of recurring themes that worry me. People have been too quick to jump to the wrong conclusions, and many remain convinced that children are being used as guinea pigs for an untested and potentially dangerous vaccine.

There are many sensible voices out there, but they are drowned in a sea of prejudice. On one forum, an independent virologist was trying to explain the link between the human papilloma virus (HPV — the infection that the vaccine protects against) and cervical cancer when one of her fellow posters launched into a tirade about vaccination being part of a plan to reduce the world’s population by 80 per cent. How on earth do you have a sensible discussion with such a crackpot?

And then there is a chiropractors’ forum suggesting that HPV has nothing to do with cancer of the cervix. A stance that they support by pointing out that most women with the virus don’t get cervical cancer, so how can it cause the disease? I suppose they apply the same primary-school logic to smoking and drink driving. Most smokers don’t get lung cancer and most drink drivers don’t get killed in car accidents, but that does not rule out cause and effect.

I also discovered a widely held belief that Cervarix is a cheap, second-rate vaccine that has already caused a number of deaths in the United States, where the authorities are supposedly considering withdrawing it. Actually Cervarix isn’t even available in the US. The national programme there uses Gardasil — a similar vaccine that offers additional protection against genital warts. Most doctors would have liked to have seen Gardasil used in the UK, too, but for that additional protective effect against warts rather than any improved safety.

The Department of Health almost certainly chose Cervarix on the basis of cost, but when it comes to protecting against cancer it is not a second-rate vaccine; indeed there is some suggestion that it may even be better than Gardasil.

I am all for healthy scepticism, but I have had enough of the scaremongering. If people choose not to be vaccinated then that is their right and it should be respected. But that has to be an informed choice based on facts, and vaccines should be considered in the same light as other medical interventions — it is the balance of benefits and risks that is critical.

Does the protection offered by the vaccine outweigh the risk of a serious reaction that could endanger your health? In the case of HPV vaccination, the answer is a resounding yes. The average British woman has around a 1 in 150 chance of developing cervical cancer during her lifetime, and then a 1 in 5 chance of going on to die from it.

Now set that against the likelihood of problems developing as a result of being vaccinated. There have been no fatal reactions from the vaccine in the UK, despite 1.4 million doses being administered in the last year. And while there have been more than 4,000 adverse reactions reported, most are minor. Frankly, given the hysteria that surrounds the current programme, I am surprised that there have not been more.

A few weeks ago I visited a girls’ school where six school nurses were vaccinating a group of teenage girls in the sports hall. The noise was incredible — a mixture of chatter, nervous laughs and screams — as the girls came forward (often in groups of two or three for moral support) to receive their jab. Such was the tension in the air that if one of the girls had fainted, I would not have been surprised if a sizeable proportion of her classmates had followed suit, and another 20 or so adverse reactions would have been reported.

But why are we so worried about vaccines, while seeming to accept much more serious side-effects from other medicines? Drugs from the non-steroidal anti-inflammatory family, such as ibuprofen and diclofenac, taken to ease pain and stiffness, kill between 2,000 and 3,000 people every year in the UK, and put many thousands more in hospital. It is a subject that I have written about numerous times, but it just doesn’t seem to catch the public’s imagination.

A CT scan of the abdomen produces enough radiation to trigger a cancer in as many as 1 in every 2,000 people scanned, yet I have patients who request one as part of a private health screen. Many of those same people are now struggling to decide whether or not to allow their daughter to have the HPV vaccine. They opt for an intervention with a very high risk/benefit ratio, yet eschew one with a very low ratio. Where is the sense in that?

Modern medicine is not perfect and doctors must do everything to ensure that they do far more good than harm. But if avoidance of harm becomes our main driver then the simplest course of action would be to do nothing, which in the longer term would do far more damage.

Vaccination against cervical cancer is a case in point — we can prevent every adverse reaction by halting the programme today, but the payback will be thousands of unnecessary deaths later.

E-mail your health questions to drmark@thetimes.co.uk or write to times2, 1 Pennington St, London E98 1TT

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