Leading doctors have warned children are at risk of missing out on key vaccinations and check-ups because their parents have not signed them up with a surgery.
Official NHS figures show there are about 3,262,000 newborns and children under five registered with GP practices in England.
However, separates figures from the Office for National Statistics (ONS) put the total number of children aged four and under at 3,385,000.
The difference between GP list and population figures suggest that around 123,000 children - four per cent of the population in England - are not on a GP’ practice register.
Professor Russell Viner, President of the Royal College of Paediatrics and Child Health, has urged parents to ensure their children are registered.
She said: “I find it deeply concerning that so many children appear to be unregistered with a GP at a time where we are seeing an emergence of preventable and deadly diseases such as the measles, record levels of childhood obesity and its associated conditions, and with 34 per cent of all child deaths in the UK considered avoidable - the vast majority of which are in infancy.”
The figures show that more than 4,000 children in outer areas of Bradford are not on the GP register.
Some 21,605 newborns and children under five are registered in the NHS Bradford Districts Clinical Commissioning Group (CCG) area. ONS figures show a population aged four and under of 25,670.
The figures also suggest around 650 children in the Doncaster CCG area and 580 youngsters in Sheffield are not on the GP register. The NHS offers regular health checks for babies until they are two-years old to monitor their development.
Youngsters are also given a personal child health record, known as a red book, in which parents and health professionals keep a log of their vaccinations and measurements.
In 2017-18, just 87 per cent of children in England had received both the recommended MMR jabs - which protects against measles, mumps and rubella - by the time they turned five.
At least 95 per cent coverage is needed to lower the risk of an outbreak, according to the World Health Organisation.
A monthly snapshot of GP patients was taken on January 1, while the most recent population estimates are for mid-2017. This means the number of children not on a GP register is an estimate.
However, the number of GP patients is generally higher than the actual population because many patients are on multiple GP registers as a result of moving house, or are not being removed after they die.
Prof Viner added: “Registering a child with a doctor can be life-saving or, at the very least, life-changing. It will mean parents get important vaccination and health check reminders, their child’s weight and development monitored and concerns acted upon quickly.
“If required, access to specialist NHS healthcare can be arranged. I urge all parents to register their child with their local GP and, if unsure, visit nhs.uk to find out more.”
NHS England pledged to increase the number of doctors in general practice by 5,ooo as part of the GP Forward View.