More than one in 50 babies has a birth defect - almost double the previous estimate, according to the most comprehensive report of its kind.
Previous figures have suggested one in 80 babies suffers a defect, which include Down's syndrome, congenital heart disease and neural tube defects such as spina bifida.
The report, from the British Isles Network of Congenital Anomaly Registers (Binocar), covers five registers of defects in England and Wales.
It includes babies born with a defect as well as those babies where the defect led to a termination of the pregnancy.
The researchers estimate there were at least 14,500 babies with birth defects in England and Wales in 2009.
Joan Morris, professor of medical statistics at Queen Mary, University of London and editor of the report, said researchers did not believe the overall incidence of birth defects is on the rise.
"We know that the incidence is not increasing," she said. "What we are now saying is that we have good figures on what it actually is."
However, she said large parts of the country, including London, do not submit any data, making it difficult to identify whether these regions are experiencing an increase in any types of defect. The report included data from five regional registers, but no registers exist in London and the South East, the North West and East Anglia.
A spokeswoman for the Department of Health said: "Parents who are fit and healthy at the start of pregnancy generally have healthier babies.
"Because of the risks, pregnant women or women trying to conceive should try to avoid drinking alcohol and stop smoking, eat a balanced diet and maintain a healthy weight."