They warn that newborns may develop infections from exposure to vaginal bacteria, and suggest that encouraging breast feeding and avoiding unnecessary antibiotics may be much more important.
The term vaginal seeding describes giving babies a swab of vaginal fluid after they have been born by caesarean.
The theory is that this boosts beneficial gut microbes that keep our immune systems healthy and so may reduce the risk of developing conditions such as asthma, food allergies, and hay fever in later life.
"The potential benefits of vaginal seeding have recently been reported in the press and, as a result, demand has increased among women attending our hospitals," write Aubrey Cunnington, senior lecturer at Imperial College London and colleagues, in an editorial.
But they point out that there is currently no firm evidence that vaginal seeding is beneficial to the infant - and warn that newborns may develop severe infections from exposure to potentially harmful vaginal pathogens from the mother.
As a result, they have advised staff at their hospitals not to perform vaginal seeding because they believe "the small risk of harm cannot be justified without evidence of benefit."
However, they acknowledge that mothers can easily do it themselves and say under these circumstances "we should respect their autonomy but ensure that they are fully informed about the theoretical risks."
Parents should also be advised to mention that they performed vaginal seeding if their baby becomes unwell "because this may influence a clinician's assessment of the risk of serious infection," they add.
"Parents and health professionals should also remember that other events in early life, such as breast feeding and antibiotic exposure, have a powerful effect on the developing microbiota," they note.
And they conclude that "encouraging breast feeding and avoiding unnecessary antibiotics may be much more important than worrying about transferring vaginal fluid on a swab."