Women who go to their family doctors with a vaginal discharge often come out of the surgery with the wrong prescription. Experts say that most GPs assume the only discharge a woman in a steady sexual relationship could have is thrush, which is uncomfortable, but harmless.

Recent studies, however, are beginning to challenge the view that thrush accounts for 80 per cent of all cases of vaginal discharge. Most women have had thrush at some stage in their lives, but doctors now believe that a third have or have had something much more serious.

Many could have bacterial vaginosis, or BV, which is being linked increasingly with a plethora of gynaecological problems including miscarriage, breast abscesses, premature births, heavy and painful periods and, in rare instances, pelvic inflammatory disease, which could lead to infertility. It is also associated with chlamydia, a sexually transmitted disease of men and women, and cervical dysplasia, cell changes of the cervix which can precede cancer.

The latest evidence is perhaps the most dramatic. New research by Dr Phillip Hay, consultant in genito-urinary medicine at St George's Hospital, south London, shows that a pregnant woman with untreated BV is five times more likely to have a late miscarriage or a premature baby than a woman without BV.

In his paper, to be published next month in the British Medical Journal, Dr Hay says that if pregnant women were routinely screened for BV it could cut the rate of late miscarriage and premature birth by 30 to 40 per cent.

A study published in July by Anona Blackwell, consultant in genito-urinary medicine at Singleton Hospital Swansea NHS Trust, indicated that women with untreated BV undergoing abortions have an increased risk of pelvic infections afterwards and she advises doctors to carry out swabs for BV after a termination, Caesarean or any other gynaecological surgery. BV often goes undetected because of the embarrassment of the patients.

'The smelly discharge causes an awful lot of mental distress to patients,' says Dr Blackwell. 'You can smell it the moment they come into the room. I had one poor lady who only had sex with her husband in the bath because of the unpleasant odour.'

Thrush and BV are quite distinct: thrush, a fungus infection caused by candida, is curdy and white, causing severe itching around the outside of the vagina and little or no odour. BV is a bacterial infection resulting from a decrease in the beneficial bacteria, such as lactobacilli, and a glut of other bacteria. The main one is gardnerella, found in 90 per cent of cases. Symptoms are a thin, watery yellow or green discharge with a strong 'fishy' smell. Unlike thrush, this infection does not cause itching.

In fairness, BV is not always so easy for the GP to diagnose. Women often wash so scrupulously before visiting the surgery that they remove the most significant symptoms, says Sally Hope, chairwoman of the Primary Care Group in Gynaecology.

No one knows just why the ecology of the vagina suddenly changes - BV can disappear spontaneously - but it seems more common in sexually active women. The higher the number of partners, particularly when condoms are not used, the more likely a woman is to get it.

But the story is complicated. While BV may be unknown in nuns or virgins, it is not a sexually transmitted disease in the traditional sense, passed from man to woman and woman to man. Treating the male partner with antibiotics has little or no effect.

Increasingly, GPs are recognising that the specialist knowledge of the GU doctors is the fastest track to a cure. At these centres BV can be diagnosed cheaply and on the spot in the microscopy units.

Even if a GP does take a swab, microbiological analysis at a laboratory may not pinpoint BV. The vaginal secretions from the swab are grown in a culture and the bacteria identified. BV is caused by an overgrowth of anaerobes, bacteria which thrive in an oxygen-free environment, such as the vagina. To be cultured properly, these must be grown in specialist conditions in which the oxygen is reduced.

'Sending swabs to the standard laboratory is only any good for thrush and the sexually transmitted diseases. It is no good for diagnosing BV,' says Dr Blackell. 'As a result, most women are reassured that nothing is wrong when there may be potentially serious consequences, including complications for future pregnancy.'

But if GPs mistakenly treat BV as if it were thrush, many women misdiagnose their intermittent bouts of BV as thrush and buy inappropriate over-the-counter treatments. The availability of thrush preparations without a prescription concerns GU specialists.

Dr Simon Barton, GU consultant at the Chelsea and Westminster Hospital, last week expressed his fears at the Clinical Overseas Congress of the British Medical Association, meeting in Calgary, Canada. 'Fifty per cent of women attending a clinic with a discharge had attempted to treat themselves. Proper diagnosis and appropriate treatment is good medicine. There is no substitute.'

He is also concerned about the possibility of self-diagnosis kits going on sale. 'The technology exists. Doctors might well be asked to get involved in trials to test them. This is something we have to resist or we will do our patients a great disservice.'

The news is not all bad. The clinics are getting better at treating BV with antibiotics. The most commonly used prescription drug - metronidazole - tastes unpleasant, can cause nausea and vomiting and reacts badly with alcohol. However, a new antibiotic cream, Dalacin, containing the powerful antibiotic clindamycin, was launched last month, on prescription, and has few side effects. It is inserted high up into the vagina once a day for seven days. Both drugs claim a cure in seven out of 10 cases.

But Dr Blackwell says: 'If you have symptoms, go to your GU clinic and find out what's causing it. More research needs to be done to convince doctors of the importance of this condition.'