A study of 11,532 infants, published in the International Journal of Obesity, showed children under six months who were given antibiotics were heavier in later years.
Researchers say the drugs could be affecting bacteria in the gut, leading to weight changes.
However, they say more work is needed to confirm there is a link.
Bacteria living on people greatly outnumber the body's own cells and there is a growing interest in how this "microbiome" affects human health. In extreme circumstances there are even examples of doctors transplanting faecal matter in order to introduce healthy bacteria into the gut, treating infections when other methods have failed.
'Kill off bacteria' In this study, children who had antibiotics between birth and the age of five months were slightly heavier between the age of 10 and 20 months. After 38 months they were 22% more likely to be overweight.
One of the researchers, Dr Leonardo Trasande from New York University School of Medicine, said: "We typically consider obesity an epidemic grounded in unhealthy diet and exercise, yet increasingly studies suggest it's more complicated.
"Microbes in our intestines may play critical roles in how we absorb calories, and exposure to antibiotics, especially early in life, may kill off healthy bacteria that influence how we absorb nutrients into our bodies, and would otherwise keep us lean."
Microbiologist Dr Cormac Gahan, from University College Cork, said there was certainly a lot of interest in the area, "but it is very early stages for this type of work".
He said changing gut bacteria could alter weight by "a direct effect on energy extraction" or by "influencing hormones".