More than 4,000 babies a year are born with congenital heart disease, which can be life-threatening if it is not treated quickly, resulting in around 200 deaths each year.
At the moment, pregnant women have tests to check for such problems, but just one in three cases are detected before birth.
The UK National Screening Committee (UK NSC) has recommended a pilot scheme to screen newborns within hours of their birth.
The pulse oximetry test uses a clip placed on a baby's fingers and toes to measure the amount of oxygen in their blood.
Experts said the pilots in six parts of the country will take a year, and if they prove effective, the programme will be expanded nationally.
Charities said the tests were 'quick, painless and cheap' and had been found to detect more than 90 per cent of life threatening heart defects at birth.
Anne Keatley-Clarke, Chief Executive of the Children's Heart Federation said: "Congenital heart disease is the most common birth defect, yet only a third of these conditions are detected before birth during a mother's pregnancy scan.
"This simple test can prevent many babies born with life-threatening conditions from leaving hospital without being diagnosed. Detection at birth means babies can receive treatment early helping to save lives, reduce physical harm and prevent distress to families."
The charity said it hoped the national programme would be introduced as soon as possible, so that no baby dies needlessly because their condition goes undiagnosed.
The equipment is already available in every hospital and currently around 20 per cent of hospitals already offer the test to all newborns.
The pilot scheme will examine the impact of routine screening on rates of mortality and disability.
Dr Anne Mackie, Director of Programmes for the UK NSC, said: "This is an exciting prospect. Pulse oximetry has the potential to detect more babies with congenital heart defects to save lives and make sure babies get the care they need before they become seriously ill.
"However the test will also identify many, many other babies with low oxygen. Some will need care for other problems and some will not be ill at all."