Over the years, the Prince of Wales has done much to put complementary medicine on the map. Last weekend in this paper, he argued eloquently for more access to traditional, natural approaches to the prevention and treatment of allergies. Allergies clearly are an important healthcare issue. Soon every second Briton will suffer from one or more. Allergic reactions are at the root of conditions ranging from a simple rash to a life-threatening anaphylactic shock, and from chronic asthma to short episodes of hay fever. The Prince has repeatedly advocated an approach now often called "integrated medicine". He feels strongly that complementary therapies should be available for all, not just those who can afford it.

The hardline opposition's response to the Prince's latest contribution to the debate was instantaneous: "... his latest intervention merely confirms our view that alternative medicine should remain the luxury of the well-to-do hypochondriac," reported the Sunday Telegraph the following day. This little battle of words exemplifies how controversial complementary medicine still is.

For 10 years, it has been my job as Britain's first and only professor of complementary medicine to try to piece together the evidence for or against complementary treatments. In doing this, we struggle for objectivity the best we can. Debates such as the current one show how difficult this task can be. They may focuspeople's minds but they rarely bring us any closer to defining what works, what is promising and what should perhaps be considered obsolete.

To achieve this goal, we need detached, well-trained scientists who are interested in the truth and can distinguish quality research from polemic spin.

So how effective is complementary medicine in treating allergies? The hardliners will be amazed to hear that not all is black. When researching this area, the first striking finding is that quite a few rigorous clinical trials, about 50 in total, have been published in the area of asthma alone. The often-voiced opinion, "nothing has been researched", is not correct. The second finding is that the results of clinical trials are rarely uniform. In fact, they are full of contradictions. It is therefore essential to resist quoting selected studies but look at the totality of the evidence available. If we do just that, we discover some surprising facts.

Here is a summary of the evidence related to asthma.

There is no convincing evidence that acupuncture or chiropractic are useful. In fact, the best evidence suggests that they are probably of no real value.

For some therapies, including autogenic training (a self-help technique based on auto-hypnosis), homeopathy, relaxation and yoga, research is inconclusive.

Encouraging, in some instances even compelling evidence, however, has been reported for biofeedback (a technique that aims to put normally unconscious information under our conscious control), breathing exercises (including the Butekyo technique, a new method for preventing hyperventilation), allergen avoidance diets, several herbal treatments, hypnotherapy, massage and meditation.

A closer look at some of this evidence is revealing. A Cochrane review, usually the best-quality evidence one can find anywhere, of acupuncture trials for asthma included seven good clinical trials with a total of 174 patients. The authors' conclusion was sobering: "It is not possible to make any recommendations." Similarly, a Cochrane review of homeopathy for asthma showed "not enough evidence to reliably assess the possible role of homeopathy in asthma". Our own study in this area, published after this review, also failed to yield any evidence in favour of homeopathy.

With other forms of allergy-related conditions, the evidence is also far from straightforward. Perhaps 20 clinical trials are available for hay fever: they show inconclusive evidence for acupuncture; negative evidence for diets and fish oil; and promising data for some herbal medicines and homoeopathy. In the area of atopic eczema, another allergy-related disease, there is inconclusive evidence for diet, Chinese herbs, evening primrose oil and German chamomile. Promising evidence, on the other hand, exists for autogenic training, biofeedback and hypnotherapy.

This state of affairs, it seems, is neither black nor white; this is an important message for all who discuss complementary medicine.

Those who reject complementary medicine as a matter of principle are misguided. There simply are no good reasons why we should not be able to find a few gems among the 400 or so different therapeutic approaches used under this umbrella. Just because we don't understand how something works, does not mean that it doesn't work. And the tools of evidence-based medicine are well suited for identifying the gems among the rubble.

But many providers of complementary medicine are still overtly or covertly against the scientific investigation of their patch. They insist that complementary therapies are too subtle, holistic or individualised for rigorous research. If this were true, they should be honest and admit that this takes complementary medicine into the realm of religion - medicine, by definition, does not defy science.

Research into complementary medicine should be considered a priority. We know that about a quarter of the UK population uses it and spends roughly £1.6bn per year doing so. We also know that some treatments show considerable promise and others are associated with significant risks. To me, these indisputable facts indicate that research is an ethical imperative. And the two most important research questions clearly relate to efficacy and safety.

The mention of potential harm sends shivers down the spine of complementary practitioners. They feel that their approaches are so much safer than anything that mainstream medicine has to offer. In many cases this may be true, in others, however, not. Safety, I would argue, is far too important to leave to conjecture; we need evidence. Even relatively minor side-effects of, for instance, a herbal medicine, weigh importantly if the potential benefit is small or uncertain. In other words, the ultimately relevant question is, does complementary medicine generate more good than harm?

The answer cannot be found without a commitment to and investment in rigorous and independent research. One reason why the evidence in complementary medicine is so often inconclusive, or at best promising, lies in the fact that few trials have been properly funded. I estimate that for every 100 trials in conventional medicine fewer than one exists in complementary medicine. My unit is generally seen as the best supported one of its kind in the UK, but we too struggle when it comes to conducting clinical trials. Less than 1% of the UK's research budgets go into complementary medicine research.

Our work is often seen with suspicion by proponents of complementary medicine. Some feel that it is not as supportive of their cause as it should be. At the root of this, I suspect, is a fundamental misunderstanding about the role of medical science. Its primary allegiance cannot be with one or the other interest group. It can only be with the quality of the work and, crucially, with the patient.

If we show, for instance, that homeopathy is not effective in treating asthma, this is perceived as a negative result by practitioners. On closer scrutiny, it turns out not to be negative at all. It enables patients to make informed choices and opt for treatments that do work. Surely this is a positive step towards optimal healthcare. What may be negative for practitioners is not necessarily negative for patients or for public health. Science that adopts a creed stops being science, and much of the current research in complementary medicine is exposed to this danger.

If we take the primacy of the patients seriously, we also might have some doubts about the presently fashionable notion of "integrated medicine". The Prince of Wales's Foundation for Integrated Health advocates as its primary aim the adoption of complementary therapies into routine healthcare. It has provided a most welcome boost for complementary medicine in the UK. But few people question the principle of integration. Should we not first make sure that these therapies are safe and effective? The NHS might end up paying dearly for treatments that are not worth their money. So let's do the science first and the integration next - it's what we call "evidence-based medicine".

To make the advances that we so badly need in this area, we must realise that complementary medicine and scientific research are not opposed to each other; evidence-based complementary medicine should no longer remain a contradiction in terms. And what complementary medicine today needs most are critical evaluation and adequate funding.

· Edzard Ernst is professor of complementary medicine at the Peninsula Medical School, Universities of Exeter and Plymouth. He will be writing regularly for the health pages.