The study involved more than 5,700 healthy children ages 2 to 6 who visited pediatricians in Rome between 2011 and 2012.
Of these children, about 600 had become overweight or obese within the last year, and the researchers ran detailed blood tests on about 200 of these children for the study.
They found that nearly 40 per cent of these children had at least one abnormal reading in their metabolism - such as high blood pressure, high cholesterol, elevated blood sugar or low levels of "good" cholesterol - which, in studies of adults, have been linked with an increased risk of heart disease and diabetes.
Obese children with such abnormal results also had a higher body mass index (BMI) than obese children without metabolic abnormalities, the study found.
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The findings show that the metabolic abnormalities linked with obesity are present in young children, even though these children have only been overweight or obese for a short period of time, the researchers said.
"Our results suggest that the risk for metabolic abnormalities related to obesity begins to manifest early in the natural history of weight gain," the researchers, from the Bambino Gesu Children's Hospital in Italy, wrote in the journal JAMA Pediatrics.