They found that smoking while pregnant increased the risk of having a baby with missing or deformed limbs by 26%.
The risk was raised by 28% for clubfoot, 27% for gastrointestinal defects, 33% for skull defects, 25% for eye defects, and 28% for cleft lip or palate.
A condition called gastroschisis, which causes parts of the stomach or intestines to protrude through the skin, carried the highest potential risk.
Smoking while pregnant increased the likelihood of giving birth to a baby with the condition by 50%.
The study, which looked at a total of 174,000 cases of malformation, was published online in the journal Human Reproduction.
Despite health warnings about the dangers of smoking while expecting a baby, 17% of pregnant UK women, and 45% of those under 20, still smoke.
Lead author Professor Allan Hackshaw, from University College London, said: "People may think that few women still smoke when pregnant. But the reality is that, particularly in women under 20, the numbers are still staggeringly high.
"Maternal smoking during pregnancy is a well established risk factor for miscarriage, low birthweight and premature birth. However, very few public health educational policies mention birth defects when referring to smoking and those that do are not very specific - this is largely because of past uncertainty over which ones are directly linked."