Australian and UK doctors are warning mothers who give birth by caesarean about the health risks of "vaginal seeding".

There's a growing trend for mothers who give birth by caesarean to cover their newborn in vaginal fluid in an effort to transfer good bacteria, but doctors warn it could be doing more harm than good.

Demand for "vaginal seeding", where a baby is given a swab of its mother's vaginal fluid after a caesarean birth, is on the rise around the world.

Theoretically it transfers beneficial microbiota from mother to baby, which can boost the baby's immune system and might reduce the risk of developing asthma, hay fever or allergies later in life.

But some Australian and UK experts have argued in an editorial published in medical journal The BMJ on Wednesday there's no clear evidence of any benefit.

They also warn that babies exposed to vaginal seeding could pick up harmful bacteria that might lead to infections like herpes, chlamydia and gonorrhoea.

The baby could also pick up group B streptococcus, which is present in about 20-30 per cent of pregnant women and is the most common cause of neonatal sepsis.

Dr Jonathon Darby, an infectious diseases physician at St Vincent's Hospital in Melbourne and one of the paper's authors, told AAP these uncommon but serious side effects outweigh the very small potential benefit.

"Whilst these are rare, unusual events, you just have to see a case of something go wrong to realise perhaps we should be a little bit more cautious," he said.

In many countries, including Australia, not all pregnant women were screened for these pathogens, the paper said.

"We think there's sufficient risk where many women don't know they carry pathogens such as sexually transmitted infections," Dr Darby said.

About one in three Australian births is by caesarean section, a rate that has increased over the past 20 years to be one of the highest in the world.

Dr Darby said vaginal seeding had only appeared recently and was still an uncommon practice.

"We became aware of it about 12 months ago. Some women in our hospital were asking about it," he said.

"Many are doing it without asking. They're looking at blogs and finding out how to do it.

"They know that conventional medicine wouldn't condone it."

The experts recommend parents advise clinicians they performed vaginal seeding if their baby becomes unwell as this might change the assessed risk of a serious infection.

Parents should also remember that breast feeding and avoiding unnecessary antibiotics have a powerful effect on the developing microbiota, they say.