Research has found that teenage boys are displaying high blood pressure and high cholesterol, directly related to being overweight and unfit.
The study of teenage boys, carried out at the centre for Preventative Medicine at DCU, has highlighted the serious health problems that overweight teenagers are facing.
Professor Niall Moyna carried out the study, which he says was unique because the children were examined for signs of heart disease not just risk factors.
"We looked at the arteries in the neck, that supply the brain, and we also looked at the arteries in their arm, which tells us what's happening in their heart.
"We found in both, that the unfit kids, had higher levels of plague in the arteries, increasing the risk of stroke."
The results for boys who were classed as "moderately fit" and "high fit" did not differ, an indication any form of exercise reduced the risk of heart disease.
Previous studies have shown that the damage can be undone but there is a small window of opportunity, according to Professor Moyna.
"Children have great plasticity and the studies show that up until their mid 20s they can reduce this. But we all know it's very difficult to change a behaviour. It's all about getting children to adopt health behaviours in the first place."
The teenagers examined had taken part in the Schools' Fitness Challenge, which is now in its fourth year.
As part of the programme students have their initial fitness levels measured, before undertaking a six weeks of training. Afterwards their fitness levels are tested again.
Last year 13,067 students participated in the challenge.
Secondary schools interested in the 2015 challenge can register online on Aviva's schools fitness challenge.
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