The impact of exercise on body fat differs for boys and girls, suggests research published ahead of print in the British Journal of Sports Medicine.
Recommendations on exercise to curb the rising tide of obesity in children have tended to take a unisex approach, say the authors.
The findings are based on a random sample of 224 children aged between 7 and 10 at 12 schools in the Republic of Ireland.
One in five children was overweight, and 6% were obese, figures which are significantly higher than those of other European countries, say the authors.
More boys than girls were obese.
Cardiorespiratory fitness was measured in all the children, using a validated running test, and the amount of exercise taken over a period of four days assessed in 152.
Boys exercised hard twice as often as girls. On average, they spent more than an hour a day, exercising vigorously. Girls spent just over half an hour a day.
Running at 9 km per hour, or its equivalent, was classified as vigorous exercise.
Overall, all the children who scored well on measures of cardiorespiratory fitness were significantly leaner and had smaller waists than those whose fitness levels were poor.
Waist size is important, say the authors, because midrift fat is associated with certain metabolic changes, which in turn are linked to poorer cardiovascular health.
Boys tended to be more physically fit than the girls. But the amount of hard exercise taken regularly had a direct impact only on the boys' weight.
Unlike the girls, those boys who did the least hard exercise were the fattest. And those who led a predominantly sedentary lifestyle had the thickest waists.
The authors suggest that the current measure of body mass index (BMI) may be inadequate, by itself, to determine the extent of cardiovascular risk in children and adolescents.