The composition of gut bacteria - known as the microbiome - has been linked to various aspects of human health, including obesity.
To study the potential relationship between taking these kinds of drugs in early childhood and the development of obesity, the researchers analysed medication prescribed to 333,353 children aged between zero and two between 2006 and 2013.
But of the 47,000 who went on to become obese, almost 90 per cent had been prescribed either antibiotics or antacids.
According to the study, boys born by C-section are at greater risk of developing obesity.
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Some 72.5 per cent had been prescribed an antibiotic, just under 12 per cent...
Researchers calculated that youngsters were 26 per cent more likely to be diagnosed with childhood obesity if they had been prescribed an antibiotic. This association persisted, irrespective of antibiotic type, and strengthened with each additional class of antibiotic prescribed.
The average risk factor for obesity rose by 26 per cent for antibiotic prescriptions, but by only 1 or 2 per cent with antacids.
But the researchers also pointed out that over prescription of both antibiotics and acid suppressants, including in young children, is "a significant problem".
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Because the study is observational it can not establish cause but the authors wrote: "We found that outpatient prescriptions for antibiotics and acid-suppressing medications within the first two years of life are associated with the development of early childhood obesity".
Antibiotics and acid suppressant medications can alter the type and number of bacteria present in the gut.
Dr Max Davie, officer at the Royal College of Paediatrics and Child Health, said: "Childhood obesity levels in the United Kingdom are at crisis point with one in three children overweight or obese by the time they leave primary school".
"We are also battling antibiotic resistance so any avoidable doses throughout the life-course would be beneficial to the cause".
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Dr Max Davie of the Royal College of Paediatrics and Child Health said the United States research did not take into account other causes of child obesity such as their home environment or mother's weight.