One of the last surviving catch-phrases of the 1980s was consigned to the verbal scrapheap in January. "Yuppie flu", still occasionally used as a macho way of dismissing the crippling symptoms of chronic fatigue syndrome (CFS), was officially declared unacceptable. A working party set up by the chief medical officer (CMO) had laboured for three years to produce a report, which concluded that, far from being a malingerer's charter, CFS should be recognised as a chronic and treatable condition.

Sir Liam Donaldson, the CMO, acknowledged that, in the past, sufferers of CFS, or myalgic encephalomyelitis (ME), had all too readily been "dismissed as hypochondriacs and urged to get better on their own". No longer, the report declared, will it be acceptable for clinicians to state that they "don't believe" in CFS/ME. While the media coverage generally represented this as some sort of resolution of an odd medical anomaly - most of the patients clearly aren't faking it - a more accurate description would be a temporary ceasefire in a long-running battle.

A glimpse of the infighting behind the scenes was provided by the resignation of six of the working group just before publication, together with a few bland comments by the CMO about a larger than usual postbag on the issue. But none of this conveys the depth of feeling involved. There was no mention, say, of a vendetta by a group of patients against one of the leading consultants in the field. And no acknowledgment of a professor emeritus so infuriated by a leaked early draft of the report that, in defiance of protocol, he posted a devastating critique on the internet.

Breaking the embargo was regarded as heroic by the radical wing of the CFS community, and outrageous by at least one of the patient groups. Calls for legal and disciplinary action filled the internet news groups for weeks. It is worth remembering that these are not political activists, but many are desperately ill people - the debilitating effects of CFS have been described as worse than having a heart condition. It was the vendetta against a leading consultant, however, that provided my own introduction to the CFS battlefield. One morning, two bulky packages thudded on to my doormat. Their combined 400 pages were a cry of rage, channelled into the impersonal format of an academic critique. Rather quaintly, they were entitled Denigration By Design: Review With References Of The Role Of Dr Simon Wessely In The Perception Of Myalgic Encephalomyelitis (ME).

Once past an initial disclaimer about there being "no personal animosity whatsoever directed at Dr Wessely", the authors of the densely typed and impressively referenced pages launch into their real business: a sustained attack on Wessely's professional competence, his ability as a scientist and his truthfulness.

Professor Wessely, as he now is, is one of the country's leading experts in CFS/ME. I had been sent the documents as evidence that here was a tale of perfidy that needed exposing. Later, more documents came with a letter that read: "If you are able to expose just how biased, unscientific and indeed evil Wessely is, you would be regarded as a saviour of mankind."

Both Denigration... and the breaking of the embargo on the web were aimed at a single target: to gain recognition of the fact that CFS is a physical disorder, as real as tuberculosis or Aids, rather than some nebulous psychiatric disorder. But wasn't this precisely the sort of misunderstanding that the CMO's report was designed to address? And didn't the fact that it declared CFS to be a chronic and treatable condition show that the reality of the disease had been acknowledged? Well, yes, but this is where the ground starts to become rather swampy, and why the CMO's report is unlikely to result in more than a temporary ceasefire.

Joint statements by old adversaries in all walks of life are often more revealing in what they don't say, and what the CMO's report signally did not say was anything about the physical basis of CFS. It was this absence that prodded Malcolm Hooper, a professor emeritus from Sunderland university, into action. Already known for his support for Gulf war veterans, he analysed a leaked draft copy and published a blistering critique on the web. The resulting calls for lawyers and disciplinary actions can still be heard.

"Once these official reports come out they get set in stone," Hooper said in his steady and deliberate northern tones. "Afterwards, if you have a complaint, or you want to change anything, you just get referred back to the report. The assumption is that all the experts have looked at it and this is what they came up with. I couldn't let that happen. A growing body of scientific literature clearly shows that there are profound disturbances of, and damage to, the neuro-endocrine-immune systems of these patients. All that evidence was just being ignored."

For the past three years, Hooper has been involved with Gulf war illness (GWI), another condition where the patients say they are physically ill while many mainstream medics continue to maintain that their problem is essentially psychiatric. He has found himself sitting on the opposite side of the fence to Wessely, who also researches in this area. "Gulf war patients are clearly ill," says Hooper. "Fit young men walking on sticks. They have obviously been poisoned, but will anyone do proper tests for the toxins we know they have been exposed to? They will not."

Hooper has attracted a following - and it is not hard to see why. A professor of medicinal chemistry, he can talk toxins, disordered sulphur metabolism, enzyme pathways and up-rated immune responses all day long. It is the sort of language that patients in both the CFS and GWI camps yearn to hear. He is supported by a dauntingly technical website, run by the autism research unit at Sunderland University, which explains the physiological links between what have been dubbed "The Overlapping Syndromes", which include CFS, multiple chemical sensitivities and GWI. He describes them as "sharing many common symptoms, together with an emerging pattern of biochemical dysfunction... that requires non- routine tests for its identification".

He outlined for me just a few of the physiological changes in the bodies of CFS patients. For instance, some CFS patients - it is always "some", which is a large part of the problem - have been found to have lowered levels of sulphate. This makes sense of a problem that many CFS sufferers share: being unable to tolerate normal levels of certain drugs or foods. The link is that drugs and foods have to be broken down in the body, and sulphate plays a vital part in this process, especially for handling a class of chemicals called phenolics. Three substances that "some" CFS patients become abnormally sensitive to are: paracetamol, citrus fruits and the adrenalin that comes with an anaesthetic injection at the dentists - all three are phenolics.

The second link concerns blood cells. Sulphation and unsaturated fatty acids are involved with keeping the walls of cells, including blood cells, strong and flexible. Research teams in Australia and New Zealand found that not only are blood cells deformed and irregular in some CFS patients, but they also identified five different subgroups of patients with different fatty acid deficits. The teams are now trying to find links between the types of distortion and the patients' symptoms.

Is this definitive? No, it is not. Does it provide a marker for CFS? No, it doesn't. However, it may link into a research project at Dundee university, reported last year. This found that "all" - very unusually - the CFS patients examined with a very sophisticated non-invasive laser had problems with the bloodflow in the tiny capillaries just below the skin after receiving a dose of acetylcholine, one of the key chemicals of the nervous system. Could it be related to irregularly shaped blood cells? Maybe.

The sulphation story was just one of many that Hooper told me. Others related to the problems some patients have with certain lipids (fats) that also build cell walls, and with their guts, which can create toxic molecules that set off the immune system. They were all evidence for Hooper's central point - if we are ever going to find a cure, or even a treatment, we need to know more about how these pathways get messed up. And to do that we should be regularly running tests on patients' blood, their sulphate levels, the functioning of their guts, and so on.

Historically, the establishment view has been that "only limited testing is necessary". Psychiatrists have regularly warned against the dangers of "over investigation", which could make patients worse by encouraging the belief that they had a physical illness. The joint 1996 Royal Colleges Report On CFS concluded that "immunological abnormalities should not... focus attention towards a search for an 'organic' cause".

From what Hooper had seen of the leaked CMO's report, it seemed to him that history was going to repeat itself and the need for extensive testing would again be underplayed. And so he fired off his salvo.

Meanwhile, the daily reality for CFS sufferers in the UK is pretty grim. A sympathetic GP may provide some support for your symptoms, but more than 60% of patients don't feel happy with the way the medical profession has treated them. That's not too surprising, given the attitude that it's apparently acceptable to adopt in magazines aimed at GPs. Here's Dr Mary Church, writing a bright column in Pulse last October on how to deal with ME: "Never let the patients know you think ME doesn't exist and is a disease of malingerers... At the end of the consultation, I say goodbye, not au revoir. Always refer ME patients to a local expert. It's a wonderful way of passing the buck."

The only officially approved treatment in the UK, cognitive behaviour therapy (CBT), is not readily available, and its benefits are disputed. The number of psychiatrists specialising in it is tiny, and their waiting lists run at about two years. The percentage of patients who make a full recovery from CFS is estimated at about 4%. If you want your CFS treated as an illness, you will generally have to go private and/or travel outside the UK.

Dr Kenny Meirlier, at the Fatigue Clinic in Brussels, for instance, focuses on the immune system; specifically, a sequence of chemical changes that take place in our white blood cells when they are fighting off a viral infection, known as the "RNaseL" pathway. He's found evidence that in CFS patients, the key enzyme involved in breaking down the invading virus and destroying the infected cell is only half its normal molecular weight. This chemical spanner in the works has all sorts of effects at a microscopic level, which could well lead to many of symptoms CFS patients complain about.

One satisfied patient, who spent a fortune and 18 months being treated by Meirlier, is "Judy". After running an exhaustive gamut of tests on her blood, immune function and the rest, he prescribed a drug that targeted her immune system and later added antibiotics. Now she is no longer confined to bed and is starting to work part-time. "I first developed glandular fever in 1993. It made me feel very tired for months, and I never really got better," she says. "There were periods when I was okay and I got a good law degree, but I kept relapsing. I had all the standard tests for viruses and bacteria, and a rheumatologist checked me out for autoimmune problems, but everything came back negative.

"I was offered CBT, but I knew I didn't have any psychological problems, I wasn't making myself ill, I had everything to live for. I tried various alternative therapies, but nothing made much difference. By the time I heard about the clinic in Belgium, in 1999, I was in a wheelchair, I actually slept for only two hours a night and I couldn't do anything except wash and eat."

Meirlier takes a combined approach, targeting both the damaged immune system and the pathogen he believes is causing it. One drug he used until very recently is called Ampligen and is aimed at the immune system. Although it is expensive and has pretty debilitating side-effects, there has been at least one small but controlled trial to show that Ampligen is beneficial. However, it has not been licensed in the US or in the UK, so its use is still experimental. Meirlier claims that an eight-year follow-up of patients treated successfully with Ampligen found that 92% had not relapsed.

The other arm of the treatment, which has really come on stream only in the past year, targets what might be called the "missing link". It is now well established that a fair proportion of CFS cases begin, like Judy's, in the wake of some sort of viral infection. The mystery is what keeps it going? Why don't the patients recover when there is no longer any sign of the virus? "We have found that 68% of patients with CFS are also infected with mycoplasma," says Meirlier. This is a tiny bacteria-like creature damaging to the immune system. Hence the treatment with antibiotics.

Again, his claims are dramatic. "You have to take a long course, about a year, and we find that the younger ones who have had the condition for a shorter time do the best. Patients who have been ill for a long time start to develop damage at the cellular level that can't be reversed. However, about 80% of patients who take the antibiotics show a great improvement." There haven't, alas, been any properly controlled trials.

Meirlier's findings, comparing the working of the RNaseL pathway in CFS patients with that in healthy controls, were published last year in the prestigious American Journal Of Medicine. In a commentary on the paper, Anthony Komaroff, professor of medicine at Harvard, remarked that the finding was "another strong piece of evidence that is consistent with the hypothesis that the immune system is activated [in CFS patients] and that the object of the immune system's attack could be a chronic infection". As for the psychiatric approach, he went on to say, "It is time to put that hypothesis to rest."

Inevitably, the value of RNaseL as a marker for CFS hasn't gone unchallenged. Last October, the results of a UK trial looking at RNaseL levels in CFS patients were published. They concluded that it was "unlikely to form a rational basis for a diagnostic test for CFS". Meirlier's response was that the researchers had done the test wrongly. "They don't have the correct probe, because it has been patented," he retorted. "It is difficult to do, but other labs have replicated it and there is a standard procedure, which has been approved by the Food And Drug Administration."

UK experts don't take the mycoplasma connection seriously, either, referring to trials showing that it wasn't a factor. However, it is a different story in the US. The Centre for Disease Control (CDC), in Atlanta, despite initial scepticism, recently set up a large-scale programme that involves detailed testing of CFS patients for such classic signs of disease as faulty gene activity, poorly functioning hormones and damage to the immune system. One project, for example, is looking for "novel pathogens", while another is screening patients' blood samples for the DNA of mycoplasma and certain bacteria.

So, there's no shortage of research going on into the possibility that CFS patients have genuine underlying physical problems. What would Wessely have to say about it all? The man who, the radicals say, had almost single-handedly caused all this hopeful research to be consigned to scientific obscurity.

I began by quoting to Komaroff's comment that the psychiatric hypothesis was dead. Wessely's response surprised me. "Oh, it's years since anyone has denied there is a biological basis to CFS," he declared. "That's just tilting at windmills. We have been most active in looking at the biological basis of CFS." What? Was the war over? Has the psychiatric camp folded up its tents and melted away? I felt like an old Tory war-horse challenging the early Tony Blair over Clause Four and increased taxation. "We were one of the first to show there was a neuroendocrine difference between CFS and depressed patients," he said, rather proudly. "When I started out, I had been struck by the similarities between CFS and depression, but this was evidence that they were different. I was surprised, I would have thought they would be the same, but you have to follow where the results lead, and I admit I changed my mind."

Later, he assiduously emailed me a list of 23 studies involving physical markers done by his unit at King's College School of Medicine in London. "I have several grants to look at immune factors in CFS," he added. "So I'm afraid another myth goes up in smoke."

But it turned out that what Wessely meant by a biological basis wasn't quite the same as what researchers such as Hooper and Meirlier understood by the phrase. "We aren't confident about the physiological basis of ME," Wessely said a little later. "It's an ambiguous illness that you can't make black and white. It's possible that, in the future, we will have a biological basis for the disease but, until something does stand up to proper testing, we are right to be sceptical."

It was also hard to get him to speculate on what this basis might be, although he was clear about what lines of research he rejected. Problems with the energy units in cells - mitochondria - had been tested and found wanting. So had mycoplasma, retroviruses, RNaseL and a urine test. "Over the past 10 years, I have lost count of the number of objective tests that have been proposed as diagnostic markers, which have gone down the plughole. If I had £1 for every dramatic breakthrough, every miracle cure since I have been dealing with the issue, I wouldn't need to worry where my merit award is coming from."

That just leaves supporters of what the report terms the "psychosocial approach" championing CBT, which doesn't seem enough. This inadequacy was illustrated by a piece of research published last December. It was based on the well-known fact that many patients, such as Judy, develop CFS after an infection that brought on CFS-like symptoms. For example, Lyme disease, caused by the bacteria Borrelia burghdorferi , has symptoms that include fatigue, headache, muscle aches, joint aches, cognitive disorders and sleep disturbance. But instead of clearing up once the infection had gone, they persist. Why? It was the same question that had interested Meirlier. Factors identified by this new study, which involved glandular fever patients, tended to be external: being less fit, having swelling in the lymph nodes and having initial bed-rest. Graded physical activity was recommended as a way of reducing the chances of CFS developing.

Now contrast that with a study currently underway at the University of New South Wales, under a contract from the CDC, looking at exactly the same thing: patients who develop post-infectious fatigue after catching Q fever, Ross River virus or Epstein-Barr virus. The factors the Australian researchers are testing for are physiological: immune system changes, pathogens persisting in the body for an unusually long time, genetic factors and psychological factors.

It must make more sense to look at these other possibilities, rather than just the social and psychological. Of course, psychological factors may play a part - they do in every disease - but to look for them exclusively seems wilfully limited, not least because one of the abiding puzzles of the psychiatric view is why these patients, some of whom are bright, successful people, should want so drastically to limit their lives by maintaining this illusion of illness? Suggestions in the literature include "learned helplessness" and "culturally sanctioned expressions of distress". Maybe some are driven by these, but all of them?

It is undeniable that some of the Freudian explanations for conditions classed as psychiatric only a few decades ago have since been discredited. One example, understandably popular with CFS patients, is the one for Parkinson's disease. Now Parkinson's is accepted as a neurological disorder, caused by a decline in dopamine production in a certain area of the brain. But in the 1940s, a psychiatric explanation was that it was the result of "conflict between an aggressive drive to action and an equally strong internal pressure to inhibit action". The specific conflict was the result of "the wish to masturbate in the ambitious moralistic man". A century ago, hysteria was the common diagnosis for symptoms with no physical cause. (In fact, one modern writer - the professor of English, Elaine Showalter - has infamously classified CFS sufferers as hysterics, along with self-proclaimed victims of alien abduction.) All this vividly illustrates the huge fault-line that runs through modern medicine, otherwise known as the mind-body split. Traditional medical systems don't make this distinction; often, they combine the psychological and the physical in a single treatment - herbs and meditation, for example. We demand a physical cause - genetic, infectious, lifestyle - with a psychological component added. So we accept that cancer patients who have had chemo-therapy, do a lot better if they go to a support group. Heart attacks are about as physical as you can get, but a recent study found that a major predictor is whether or not you have an optimistic outlook.

Psychiatrists take stick from groups on both sides of our self-imposed divide. Patients with depression, say, often complain that their treatment is far too biologically based, and call for less drugs and for more attention to be paid to the meaning of their disorder. It doesn't seem a very big stretch to include both sides, physiological and psychological, in the way CFS is researched and treated. It might even be imminent.

As I shuttled between Hooper and Wessely in the weeks before publication of the report, it began to seem that they shared a lot of common ground. "I'm interested in running specialised tests on patients, if they can be done as part of controlled studies," said Wessely. Earlier, he'd stated that there was not "a cigarette paper's thickness" between his approach and that of the CDC and its programme into physical causes. And Hooper was happy to admit that CBT, the psychiatrists' cure-all, might be useful in some cases.

One of the radical's many charges is that the psychiatrists use this particular therapy to challenge patients' belief that they have an illness. And yet, here again, Wessely proffered an olive branch, admitting that, in the past, he had, perhaps, put things in rather an abrupt way. Rather extraordinarily for a psychiatrist, he added, "Then, I was not so sensitive to the power of language. I've changed a bit." Now he says he would never challenge anyone's belief as to what the underlying illness was, except if they thought it was Aids.

It's certain that neither side has the stomach for a style of conflict more often seen in the political arena. All the combatants have said how hurt and upset they've been by enemy action. Wessely himself recently issued a call for some sort of peace. So what are they all waiting for?

Jerome Burne is editor of Medicine Today ( www.medicine-today.co.uk). For information about CFS/ME, visit www.co-cure.org, the main information exchange forum; www.cfids-cab.org/ME/consideration.html, for a document from the authors of Denigration...; www.afme.org.uk/index.shtml, the site of one of the main UK campaigning groups, Action For ME; and www.doh.gov.uk/cfs-me.htm for details on the background to the CMO's report.