One baby in 46 has a birth defect, doctors have revealed.
A report found England and Wales has higher rates of neural tube defects such as spina bifida than many other European countries.
Overall the highest numbers of defects are in babies born to women aged 40 and over. The study, from the British Isles Network of Congenital Anomaly Registers, is the most comprehensive of its kind, covering six regions of England and Wales.
Authors estimate that there were 15,966 babies suffering defects in 2011, or 2.2 per cent of babies.
The most common anomalies were congenital heart defects, which affect at least six in every 1,000 babies. Some require major surgery and around six per cent die before their first birthday.
Neural tube defects, such as spina bifida, affect one in 1,000 babies.
The report’s authors estimated that 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, with older mothers at higher risk of having a baby with the condition.
Mothers aged 25 to 29 were the least likely to have a baby suffering any defect at 187 per 10,000 babies but in the 40 and over age group the rate was more than double at 396 per 10,000 babies.
The report collates data from six regional registers including those in Yorkshire, covering 36 per cent of births in England and Wales.
Overall, 61 per cent of defects are diagnosed before birth. Of these, 44 per cent lead to a termination.
Numbers and types of congenital anomalies have been monitored since the thalidomide epidemic in the 1960s.
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, although the likely figure was closer to one in 40.
“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,” she said.
“Currently there are no registers in London, the South East, the North West and East Anglia.”