The head of allergy and immunology at one of Australia's largest children's hospitals has issued a warning about a looming crisis in the healthcare system.

Associate Professor Alyson Kakakios, who is head of the Allergy and Immunology Department at Sydney's Westmead Children's Hospital, says the number of children with food allergies and rare medical conditions has increased dramatically in the last decade.

Doctors at the hospital have been under pressure for some time, but as the children grow older, there are worries that adult hospitals are not prepared.

Damian Scott, 18, has spent most of his life battling a range of allergies and rare health conditions and will soon leave the children's hospital to enter the world of adult health care.

Mr Scott does not have enough white blood cells to fight infections, carries an epipen to prevent anaphylaxis, and undergoes constant treatment for eosinophilic oesophagitis - a severe inflammation that scars his food pipe.

His treatment in the children's hospital has kept him alive.

"In the children's hospital, it was just always right. It always worked, it never went wrong. But with the adult hospital, I feel like they're not ready enough yet," Mr Scott said.

"Quite a few times in the past, there's been incidences where we've got doctors that don't know the full extent of what my condition is, and they make calls and it turns out it's the wrong call. We've had to get Dr Kakakios in and fix it all up for us," he said.

"I feel like we've finished that in the children's hospital, so most doctors know about the condition. But I don't know about the adult hospital."

Dr Kakakios has been caring for Mr Scott since he was two years old.

"My concern mainly relates to the lack of resources or the inadequate resources that are involved in the adult health services," she said.

"This is not to say that they're not very good in delivering what services they have. It's just that the amount of those resources is inadequate to deal with the very great increase in the allergic diseases which we've seen in the past 10 to 20 years.

"There's just not enough of them to deal with the real increase in these disorders, which are chronic disorders that we've seen over the past 20 years.

"These young infants - Damian was under two when I started looking after him - they've gone on to adult services, and there are many, many, many more like him, many more than can be adequately cared for given the requirements for their management."

Sharp rise in allergy cases

The number of children with peanut allergies has doubled in the past decade, while egg allergies are now the most common in Australia.

Twenty years ago the allergy only affected up to 2 per cent of the population. Now, it is 10 per cent.

Dr Kakakios says hygiene is partly to blame.

"It's increased in our Western societies because of the way that we live our lives, very cleanly," she said.

"We don't give the immune system enough grist for its mill, if you like. The immune system is there to protect us from infections. We live a very clean lifestyle, a very antiseptic lifestyle, which starts at birth."

There is no simple explanation for Mr Scott's conditions but they require a range of specialists including gastroenterologists, allergists, and dieticians.

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President of Allergy and Anaphlaxis Australia Maria Said says there are not enough of those specialists in adult hospitals.

"These children grow up, and there are a limited - a reduced - number of specialists to take on their care. It is a huge concern, and it really is time that allergy was seen as a national public health priority," she said.

Mr Scott and his family remain optimistic. His mother Annette Scott says the real test is yet to come.

"The problem will be if he goes through the emergency department and we don't get a specialist in the immunology or allergy area. That's when you run up against problems, because it is quite rare but becoming more common," Ms Scott said.

"But because of that, not everyone knows really well how to deal with these kids, or now adults."

The Federal Health Minister Peter Dutton was not available for comment.

A spokeswoman for the Health Department says the Government provided more than $3 million for research into food allergies last year.