Researchers studied 1255 children, including 284 born by Caesarean section.
One in six of these kids was classed as obese by the age of three, compared with one in 13 born naturally, meaning the average three year old would be 0.5lb or 0.23kg heavier.
Although the experts said further research was needed, they believed that differences in the bacteria in the gut between those born by Caesarean and those born naturally was the reason.
At present, around a quarter of women give birth by C-section in Britain, most of which are emergencies.
These mums are normally given antibiotics and this could influence gut bacteria in the baby as well as the transit through the birth canal.
It may be that gut bacteria influence the development of obesity by increasing energy extracted from the diet, and by stimulating cells to boost insulin resistance, inflammation, and fat deposits, the report suggested.
Dr Susanna Huh, of the Division of Gastroenterology and Nutrition at Boston Children's Hospital, US, wrote in the journal Archives of Disease in Childhood: "A mother who chooses Caesarean delivery on maternal request should be aware of potential health risks to her and her baby, including childhood obesity and other potential long-term risks.
"In this study, infants delivered by caesarean section had two-fold higher odds of childhood obesity, even after adjusting for maternal BMI, birth weight and other confounding variables.
"Expectant mothers choosing caesarean delivery in the absence of an obstetrical or medical indication should be aware that their children may have a higher risk of obesity."
Sue Macdonald, education and research manager at the Royal College of Midwives, told the Telegraph: "This highlights the need to avoid Caesarean sections that are not medically needed.
"Evidence is building and suggests that unnecessary caesarean sections may have detrimental effects in the short and long term for the woman, and the child."
Hmm. What do you think?
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