Test-tube babies are almost twice as likely to suffer birth defects than children born naturally, according to the largest study of its kind.
Babies conceived through IVF have a significantly higher risk of being born with heart problems and malformed reproductive systems than those conceived naturally.
The scientists behind the shocking study called on fertility clinics to routinely warn prospective parents of the dangers - claiming that far too often, they are kept in the dark.
It follows a range of other studies which have found that IVF children are more likely to suffer from cerebral palsy and autism - while boys born through IVF are more likely to be infertile.
More than 120,000 children in the UK have been born using the technique since 1992. For the latest research, scientists carried out a survey of 33 French fertility centres, collecting data on more than 15,000 births from 2003 to 2007.
They found that 4.24 per cent of children born through IVF had some form of congenital deformity - compared to the rate for children conceived naturally of between 2 and 3 per cent. This would indicate that some 5,000 IVF babies in Britain may have been born with defects.
Study author Dr Geraldine Viot said: 'This higher rate was due in part to an excess of heart diseases and malformations of the urogenital system. This was much more common in boys. Among the minor malformations, we found a five times higher rate of angioma, benign tumours made up of small blood vessels on or near the surface of the skin.
'These occurred more than twice as frequently in girls than boys.'
Dr Viot, a clinical geneticist at the Maternite Port Royal Hospital in Paris, called for more research to understand the reasons behind the increased risk, adding that 'a malformation rate of this magnitude is a public health issue'.
She said there could be a wide range of explanations, including infertility itself, ovarian stimulation, the maturing of eggs in the laboratory, or the ICSI (intra-cytoplasmic sperm injection) technique which injects a single sperm into the egg.
'We just don't know at present,' she said. 'Finding this out will be a major step towards improving the health of children born after ART (assisted reproductive technology).
Last night Josephine Quintavalle, of campaign group Comment on Reproductive Ethics, said: 'Given the degree of unnatural manipulation involved in assisted reproduction, we should not be surprised that nature still does it better.
'Infertility treatment should focus much more on restoring natural fertility to patients and far less on engineering in the laboratory. Children deserve the best.'
A spokesman for the Human Fertilisation and Embryology Authority said: 'A study in France has shown that there is a small but clear increase in risks of congenital abnormalities in children born as a result of IVF or ICSI.
'It is important that patients are informed about this but not alarmed by it.
'We keep research of this kind under review and where it suggests there may be a greater risk we share this information with patients in a clear way to help them understand the risks associated with the choices they are making.'
Article: 14th June 2010 www.dailymail.co.uk
Read more about assisted reproductive methods such as home insemination and more natural ways of conceiving, before trying IVF.