The study published in the journal PLoS One analysed data from six exercise studies involving 1,687 regular exercisers to find out the effects of regular workouts on the heart.
The results shocked and confused the scientists: in almost one in ten people tested, exercise seemed adversely to affect blood pressure, insulin levels or 'good' HDL cholesterol levels.
And in seven per cent of people, not just one but two of these risk factors for heart disease were worse as a result of exercise, the 'Daily Mail' reported.
"There is no clear explanation for this effect on a small portion of the population, but it's not a good sign," said Claude Bouchard, the study's lead author and a professor of genetics and nutrition at Louisiana State University.
He suspects it is down to genetics and advises exercisers to have their blood pressure, cholesterol and glucose checked regularly.
Regular amounts of aerobic exercise, such as running, are known to slow the unhealthy changes to the cardiovascular system that occur with age.
However, intense and prolonged endurance training for many years - for instance, for marathons or triathlons - could be damaging to the heart, an editorial review published last year in the British Journal of Sports Medicine suggested.
"Our research found that 50 per cent of long-term endurance and ultra-endurance runners, some of whom had been training for 43 years, showed signs of heart damage," said the author, Greg Whyte, professor of sports science at Liverpool John Moores University.
"It is well documented that among veteran athletes there is a higher incidence of early symptoms of cardiac disease, which might increase the risk of a heart attack," Whyte said.
"There is a build-up of collagen in place of heart muscle, and compounds of blood markers that can make someone more susceptible to unusual heart rhythms," Whyte said.
However, Whyte said people should not be worried about exercising, pointing to overwhelming evidence that it is wholly beneficial, not just for the heart but for the whole body.
In the current study, for 10 per cent of people there were enormous gains in at least one measure of heart disease risk, with some improving by up to 50 per cent.
And among those who did have adverse outcomes, there was no evidence that these led to heart attacks or other health problems.
"There will always be a few cases of people with underlying health problems and heart issues for whom physical activity can be problematic, but most people should be doing more of it, not less," Whyte said.
