"We speculate that mothers' use of antibiotics changes the balance of natural bacteria, which is transmitted to the newborn, and that such unbalanced bacteria in early life impact on the immune maturation in the newborn," said Hans Bisgaard, one of the study's authors.
Previous research has linked antibiotics taken during infancy to a higher risk of asthma, although some researchers have disputed those findings.
Dr Bisgaard and his colleagues gathered information from a Danish national birth database of more than 30,000 children born between 1997 and 2003, and followed for five years.
They found that about 7,300 of the children, or nearly one quarter, were exposed to antibiotics while their mothers were pregnant.
Among them, just over 3pc, 238 children, were hospitalised for asthma by the age of five.
The study found that by contrast, about 2.5pc, or 581, of some 23,000 children whose mothers didn't take antibiotics, were hospitalised with asthma.