When a woman in Canada gave birth to six babies earlier this year, it led to a battle between religion and medicine, between the children's right to life and their parents' right to practise their religious beliefs. Two of the babies, born 15 weeks early, died. The parents, who are both Jehovah's Witnesses, refused to allow blood transfusions, in accordance with their faith, and three of the babies were taken into custody by social workers so they could be given the treatment. Custody has now been returned to the parents, who have not been named, but they are angry at the intervention and have gone to court to prevent officials stepping in again.

In this country, the General Medical Council places great importance on respecting the religious beliefs of patients, but in cases where parents refuse consent for a child's essential care, doctors can and do go to the courts. If an adult refuses a transfusion, there is nothing doctors can do other than try alternative treatments. Jane O'Brien, head of standards and ethics at the GMC, says this can lead to distressing situations for doctors. "Sometimes they have to watch people die, but you can't treat people against their wishes."

In the 1980s, Jehovah's Witnesses set up a hospital liaison committee to help understanding between patients of the faith and the medical staff who treat them. In this country, there are around 125,000 Jehovah's Witnesses. The religion, a branch of Christianity, forbids its followers from receiving blood transfusions. Bloodless surgery - where blood loss is minimised by operating in stages or using drugs - is increasingly being used here, after it was pioneered in the US as a way of treating Jehovah's Witnesses. Jehovah's Witness church groups also raise money to buy machines that recycle a patient's own blood.

For those outside the faith, it can be difficult to understand the depth of these beliefs, which are maintained even if it means risking their lives, or the lives of their children. In 2003, 36-year-old Angela Shipperley died after complications following the premature birth of her second child, Joel, by emergency caesarian. An investigation by the Healthcare Commission found that the hospital, Northwick Park in north-west London, had failed in its care towards her. Although seriously ill, she had been moved to a ward where she could not be monitored as closely as she should have been and there was confusion over which drugs she had been given. However, her care had been made more difficult by her refusal to accept a blood transfusion.

Her widower, Alvin, also a Jehovah's Witness, believes the hospital could have offered alternatives and had been given plenty of warning that his wife followed the faith. She was repeatedly told she needed a blood transfusion, but always refused. "We both talked about it and I supported her conscientious stand," says Shipperley. And he is in no doubt that her decision to refuse a transfusion was the right one. "My faith is strengthened to have seen my wife make such a firm stand. I have no doubt that she would do exactly the same again. We do not want to be martyrs. In fact, we want the very best medical treatment available but without the use of blood."

Although no other religion takes such an extreme view of a particular type of treatment, doctors are increasingly accommodating patients' religious beliefs. With circumcision for male babies in the Jewish and Muslim faiths, doctors who oppose the practice do not have to carry it out, but should make it clear that there are other doctors who will. (Similarly, doctors are not required to carry out abortions, and pharmacists are not required by law to dispense emergency contraception if it is in conflict with their religious beliefs.)

Regardless of the arguments for or against ritual circumcision, the procedure is being performed on tens of thousands of babies every year, often by GPs with little or no training. Dr Tariq Shah, a consultant urologist, pioneered the first circumcision service on religious grounds in 1996 in an NHS hospital in Bradford, which has a large Muslim community. Although offered by the NHS, the service costs £60. Other hospitals now also offer the service.

In 2003, the Association of Catholic Women started selling ID cards (so far, it has sold nearly 29,000) that, in effect, ask doctors not to withdraw treatment if the patient is deemed to have a "poor quality of life". Catholics hold life sacred and would want to be kept alive for as long as possible. The simple blue card reads: "In case of my admission to hospital, please contact a Roman Catholic priest. I would like my nursing care to include fluids - however administered."

"Catholics would want to see a priest in hospital," says Ruth Real, secretary of the organisation. "But if you're unconscious or can't make this clear, a card like this can be useful in identifying you and your wishes. It has brought comfort to a lot of Catholics."

However, it is by no means a guarantee that artificial nutrition and hydration will be administered. The GMC's position is complex. "Giving food and water is basic care and must be provided," says O'Brien. "Where it gets complicated is where the patient is unable to swallow, and nutrition and fluids are provided through a tube, or by a drip. In those circumstances, it is classified as medical treatment. Doctors are guided by patients' wishes and it is important to discuss with them what they want, but if there is a conflict, doctors can't be forced to provide treatment if they believe it will be detrimental to the person's health."

Even something as seemingly innocuous as telling excited parents the sex of their unborn child is mired in uncomfortable cultural issues. The Royal College of Obstetricians and Gynaecologists says hospitals are allowed to tell parents the gender of their unborn child at a 20-week scan, but they are not required to. While most NHS trusts will tell parents if they ask, some have a policy of not revealing the sex of the baby.

Although the reasons given vary from time and cost constraints to the worry that parents could sue if the hospital gets it wrong, some doctors believe it protects unborn children, particularly when the parents are from particular ethnic groups, especially those of Asian heritage. Not surprisingly, many Asian women feel victimised.

Two years ago, consultant paediatrician Sudhir Sethi, who heads the child protection team in Leicestershire, said he believed a very small number of Leicester's large Asian population were going abroad to abort female foetuses because of the value placed on male children. Does he still believe this? "Globally, it's a major issue, but this country plays a very small part," says Sethi. "My focus is more on the global issue, but there is growing evidence of women from the UK going to India [for late terminations of female foetuses]. There is no data on how many women do this but I'm very much aware that it does happen. No religion promotes female foeticide, but it is ingrained in some cultures."