The highest rate is among Pacific children, especially in regions such as South Auckland, where cases are 80 times higher than in other developed countries.
Now the problem is spreading, and doctors sometimes fail to recognise the condition.
The 8-year-old who had the open-heart surgery, Kyuss Burnell, goes to a decile 10 school in the affluent Auckland suburb of Mission Bay. Last year, when he complained of a sore throat, his mother, Saphira Va'afusuaga, thought he had the flu.
"After four months of back-and-forth doctor visits, Kyuss was told by our family doctor to try going to school if he felt up to it," she says. "The next day, he was rushed to Starship [hospital] by ambulance at 4am because he couldn't breathe."
Rheumatic fever develops from a strain of streptococcus (strep throat) and, if left untreated, can cause scarring on the heart valves, developing into rheumatic heart disease.
Va'afusuaga says several doctors did not detect the tell-tale sign of a heart murmur that signals early stages of rheumatic fever.
It was not until a full chest x-ray was conducted that it was revealed Kyuss' heart valves were leaking, causing fluid on his lungs.
Within a week of being rushed to hospital and a doctor saying rheumatic fever could be "completely ruled out", Kyuss was prepped for a six-hour bypass operation to repair the damaged valves of his heart.
Va'afusuaga says parents and doctors everywhere - not just in low-income areas - need to know how to recognise rheumatic fever. "Yes, Polynesian and Maori children are more at risk, but that doesn't mean other ethnicities are immune.
"I look at my son and think, with a course of antibiotics and us having known the information we know now, he would not have ended up needing open-heart surgery."
Starship clinical director Dr Richard Aicken says Aucklanders can be confident in the ability of the region's doctors to diagnose rheumatic fever, because the region has such a high rate of the disease.
Public Health Director Dr Mark Jacobs says the throat-swabbing is targeted at areas of highest risk. "The awareness programme, as part of the broader campaign, is still in development, and will include initiatives aimed at both higher-risk groups and the broader population."
But Labour health spokeswoman Annette King says the campaign should target everyone.
"Many families, whether high or low income, will not have the knowledge or awareness of this problem," she says. "There needs to be information put into all schools, like a note in every kid's lunch box, not just lower deciles."
Saphira Va'afusuaga simply pleads for parents to listen to their children.
"I would never wish this ordeal on another family," she says. "As a mother, I urge other parents to pay attention to their kids when they have a sore throat. It's so easy to just assume it's the flu but it can be so much more sinister than that."
• Opinion: Prevention the best strategy
