One in 46 babies has a birth defect - although the figure could be as high as one in 40, according to new research.
England and Wales also has higher rates of neural tube defects such as spina bifida than many other European countries.
The report, from the British Isles Network of Congenital Anomaly Registers (Binocar), is the most comprehensive of its kind, covering six regions of England and Wales.
The authors estimate there were 15,966 babies suffering defects in 2011, or 2.2% of babies.
The most common anomalies are congenital heart defects, which affect at least six in every 1,000 babies.
Those suffering heart problems can require major surgery, and around 6% of babies with a heart defect die before their first birthday.
Neural tube defects, such as spina bifida, affect one in 1,000 babies, according to the report.
The authors estimated that overall in 2011 4,461 babies suffered heart defects, 1,739 had defects of the nervous system, 1,223 had problems with the digestive system and there were 1,143 cases of cleft lip or palate, alone or alongside other defects.
Some 1,973 babies had Down’s syndrome - a rate of 25.7 per 10,000 births - with older mothers at higher risk of having a baby with the condition.
The South East and London had the highest rates of Down’s, reflecting the fact more mothers over 35 live in these areas.
In London, the rate for Down’s syndrome was 31 per 10,000 births.
Overall, mothers aged 25 to 29 were the least likely to have a baby suffering any defect (187 per 10,000 babies), rising to 243 per 10,000 babies among the under 20s.
The figure was considerably higher in the 40 and over age group (396 per 10,000 babies).
Gastroschisis - a condition where the intestines develop outside the abdomen - affects one in 1,000 babies, the report went on.
It is more common among younger mothers and is more likely to be seen in England and Wales than in other European countries.
The report, by researchers at Queen Mary University of London, collates data from six regional registers, giving a national coverage of 36% of the births in England and Wales. Researchers then provided estimates for all of England and Wales.
The number and types of anomalies have been monitored since the thalidomide epidemic in the 1960s.
Overall, 61% of defects are diagnosed before birth. Of these cases, 44% result in a termination.
Joan Morris, professor of medical statistics at Queen Mary, University of London, said the 2011 figures did not suggest an overall increase in the number of babies suffering defects compared to previous years.
“It’s stayed pretty much the same,” she said. “One in 46 babies were thought to have a defect in 2011, although we know this is an underestimate and it’s likely to be closer to one in 40.
“Overall, our impression is that we’re pretty similar to Europe although we have higher rates of abdominal defects, particularly among younger mothers.
“People feel this is lifestyle related. Evidence suggests that risks are increased, particularly in lower body mass index mums - the thinner teenage pregnancies - but we can’t say that’s definitely the cause.
“We also have higher rates of neural tube defects than other countries but it’s not exactly clear why.”
Taking folic acid during pregnancy is known to cut rates of neural defects.
Prof Morris called for better overall reporting of defects to give a more accurate picture of what is going on.
“We remain concerned that data for substantial parts of the country, including London, are not currently monitored, meaning large regional increases in congenital anomalies could go unnoticed and their causes not investigated.
“Currently there are no registers in London, the South East, the North West and East Anglia.”
Maureen Talbot, senior cardiac nurse at the British Heart Foundation, said: “Heart disease doesn’t always wait until adulthood to strike. Sadly, some babies have to undergo serious operations before they even reach their first birthday.
“Coping with a child born with congenital defects can cause lots of stress and worry for families.
“Research is getting closer to understanding what might cause these problems but, until then, we can support families by helping them to come to terms with their child’s condition.”
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