The warning comes from a study which found that smoking damages the future fertility of sons.
It is said to be the first time conclusive proof has been found that smoking harms the developing reproductive organs of boys.
The research was carried out on mice because it would be unethical to expose pregnant women to cigarettes.
It found that male offspring of mice that smoked had a permanently reduced sperm count as well as other changes that meant they were unable to swim properly, were misshapen and so could not easily fertilise an egg.
The researchers said the findings could explain sub-fertility in men in their 30s and 40s now, who were born when there was less known about the dangers of smoking during pregnancy.
Around 25 per cent of women currently smoke while pregnant.
Lead author Professor Eileen McLaughlin, co-director of the Priority Research Centre in Chemical Biology at the University of Newcastle in New South Wales, Australia, said: "It would be unethical to deliberately expose pregnant mothers and their offspring to the toxins in cigarettes – we already know that smoking in pregnancy harms the baby in the womb – as babies are often born small and vulnerable to disease.
"So, in this study we used a mouse animal model, which directly mimics human smoking, to look at what effects the mothers smoking during pregnancy and breast feeding has on the fertility of their male pups.
"Our results show that male pups of 'smoking' mothers have fewer sperm, which swim poorly, are abnormally shaped and fail to bind to eggs during in vitro fertilisation studies.
"Consequently, when these pups reach adulthood they are sub fertile or infertile. This is the first time we have been able to prove conclusively that male baby exposure to cigarette toxins in pregnancy and early life will damage later life fertility.
"We now know that exposure to cigarette toxins directly affects the stem cell population in the testes, causing a permanent reduction in the population of sperm produced.
"We also know that oxidative stress induced by these toxins causes damage to the nuclei and mitochondria, the cell's 'power' supply, of cells in the testes and this results in sperm with abnormal heads and tails, that are unable to swim properly or successfully bind and fuse with eggs.
"Although this is a study in mice, the findings are relevant to human health as many men, now in their 30s and 40s, were exposed to cigarette toxins in the womb when it was less well known that smoking affected babies' health.
"These men have difficulty conceiving and this is associated with production of low numbers of poor quality sperm in their semen.
"Unfortunately about 25 per cent of young women today continue to smoke when they are pregnant and/or breast feeding – thereby potentially damaging their sons fertility."
Mr Stuart Lavery a consultant gynaecologist and director of IVF Hammersmith at Hammersmith Hospital, in London told the Telegraph: "We have known for many years that women who smoke during pregnancy put their babies at higher risk of adverse outcomes.
"There has been increasing evidence to show that these risks can carry long term consequences for their children.
"This well designed experiment conducted in mice has shown a reduction in the sperm parameters and fertility of the male offspring.
"As the researchers point out it would be unethical to repeat this experiment in humans however it brings additional evidence and weight to the advice that women should stop smoking not only for their own health benefit to but also to protect the long term health and reproductive potential of their children."
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