The study found obese children had 30 per cent thicker heart muscle compared to those of a healthy weight. Suffering from an abnormally enlarged organ is an early marker of heart disease.
Nearly all of the overweight babies were bottle-fed, leading experts to warn too much formula milk is fuelling soaring obesity rates.
The scans revealed fat children had enlargement and thickening in the left part of the heart – the key pumping chamber.
Scientists said the early damage could see babies doomed to early heart failure, caused by poor diets and a lack of exercise.
The findings, presented at the European Society of Cardiology congress in Barcelona, prompted calls for urgent action to tackle spiralling rates of global obesity.
In Britain, more than one third of children are overweight or obese by the time they leave primary school, along with six in ten adults. The research involved 455 children who were seen in cardiology clinics in Romania.
The country has the lowest obesity rates in the EU, with just 9.4 per cent of adults classed as obese, compared to a figure of 24.8 per cent in England.
British experts said the findings should cause alarm in the UK, given its far worse record, and trigger urgent action to tackle obesity among the young.
Tam Fry, from the National Obesity Forum, said: “When obesity exacerbates their heart health in toddlerhood, alarm bells should be ringing.”
And he said the failure to properly track the weight of children before they started school meant Britain was allowing problems to store up.
“We don’t know what the full extent might be since we have no idea of how many obese preschoolers we have here,” he warned.
“These Romanian children may well die before their parents as well as suffering life long illness: ours will be no different,” he said.
Lead researcher Dr Delia Mercea, from Constantin Opris hospital in Baia Mare said: “It’s a huge problem because obesity and overweight affects children and it’s possible that this [thickening] could lead to heart failure in time.”
The study included 54 babies below the age of 1 and 125 toddlers. All had been bottle fed, which is linked to higher rates of obesity.
Britain has one of the lowest rates of breastfeeding rates in the world with just one in three babies breastfed until six months, in line with NHS advice.
Dr Mercea said doctors should intervene to warn parents that their children’s diets could prove lethal.
“The end stage is heart failure,” she warned. Drastic lifestyle changes were needed in lifestyles across the world, she said.
“We should encourage healthy food and physical exercise. Doctors should tell parents what kind of food to give to children – not fast food, not sweets, proper food at home and natural food like fruit and vegetables.”
Lack of exercise was exacerbating the problem, she said.
“Children tend to sit more in front of the TV, computer, notepad, from very early age instead of playing in the back yard or beginning a sport,” she added.