Kids in the South Island are up to three times more likely to suffer debilitating inflammatory bowel diseases (IBDs) than their northern counterparts.

That's according to a first-of-its-kind study by researchers who say the difference could be partly put down to sunlight and its impact on vitamin D levels.

The data, collected in 2015, showed between 40 and 60 children per 100,000 had a diagnosis of an IBD - which include conditions like Crohn's disease - in the South Island.

In the North Island, the rate was between 10 and 20 children per 100,000.

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In Canterbury, 40 children in every 100,000 had a diagnosis of IBD.

Researcher and paediatrician Professor Andrew Day, of Otago University, said the difference between the islands was not fully understood, but could be due to variations in sunlight, and its impact on vitamin D levels.

It warranted further investigation, he said.

"There is a growing incidence of IBD in children worldwide but little information about rates in New Zealand children," Day said.

"Our study found quite a striking difference between the North and South Islands."

One theory was that South Island children could have lower levels of vitamin D.

This had implications for their immune system as vitamin D is involved in the production of a molecule that plays a key defensive role in the gut.

The theory was supported by European research showing colder places such as Scandinavia had higher rates of the diseases than warmer countries on the continent.

The reason for an increasing number of children being diagnosed with IBD was a subject of intense debate and scrutiny internationally, Day said.

One possible explanation was that children's diet now consisted of far more processed than whole foods.

Another was that children did not play outdoors as much and get exposure and immunity to germs, he said.

An IBD diagnosis was often a big blow for a child and their family.

"It's a lifelong condition with no cure," Day said.

"For those with more severe forms of the disease, there are often hospital stays to administer medication or for surgery.

"Some children need to have regular injections or infusions of medication."

Steroids used to be a common treatment for the condition but doctors were wary of prescribing them now because of better alternatives and steroids potential to affect growth, among other side effects, he said.

"At diagnosis now we are commonly recommending a special liquid-only diet for a period of time, and later daily ongoing medication to maintain control of the condition."

Day says his team hope to follow the prevalence study with one that measures vitamin D levels in IBD sufferers as well as their location in New Zealand.