Researchers analyzed medical records for nearly 25,000 children born in Britain between 1988 and 1999. About one-third of the women had been prescribed one or more courses of antibiotics during pregnancy.
They found that if mothers used antibiotics, the chances of their child having asthma rose by 31 percent. The chances of their child having hay fever went up by 27 percent, and the risk for eczema increased by 5 percent.
The link was even stronger in the children of mothers who were prescribed two or more courses of antibiotics: They had a 60 percent greater chance of being asthmatic.
"This is the first study to show the relationship between allergies and antibiotics during pregnancy," says lead author Tricia M. McKeever, a research assistant in the department of respiratory medicine at the University of Nottingham in England.
However, some experts caution against jumping to conclusions. The researchers could not fully determine how much of the increased risk of asthma and allergies was due to taking the antibiotics and how much was due to the infection for which the mothers took the medicine.
Another issue is the hereditary component of asthma and allergies. The most common infection the mothers had was respiratory ailments. This could mean many of them were asthmatic themselves.
"Clearly, the central problem is whether the effect they're looking at is an effect of antibiotics or an effect of infection," says Dr. Thomas Platts-Mills, an allergy expert and professor of medicine at the University of Virginia.
In recent years, evidence has been mounting for what's known as the "hygienic theory" or the "cleanliness hypothesis." The theory behind it is that exposure to germs can actually be good for you by boosting the immune system, thereby making you less susceptible to allergies, Platts-Mills explains.
However, our modern lifestyle -- including the increasing use of household disinfectants and microbiological cleaners and the overuse of antibiotics -- has made the world too sterile, Platts-Mills says.
Some believe it could be closely linked to the significant increase in asthma and allergies in children since 1960, when antibiotics became widely prescribed, Platts-Mills says: "Many of us in the medical profession believe that the use of antibiotics is excessive."
McKeever says taking antibiotics during pregnancy could kill microflora in the gut, which are believed to aid in the development of the immune system.
Depending on how you read the study, it could either confirm or refute the "cleanliness hypothesis."
"If the effect is because of antibiotics, then it supports the cleanliness hypothesis," Platts-Mills says. "But if infections in the mother increase the risk of asthma or allergies, than it's completely the opposite."
Platts-Mills also notes women took antibiotics mainly for respiratory illnesses, perhaps indicating the women had asthma and allergies themselves. Allergies have a hereditary component.
In the paper, which appears in the September issue of the American Journal of Respiratory and Critical Care Medicine, researchers say they controlled for allergies in the mother, smoking and age.
What's an expectant mother to do?
Keep the study in perspective, says Dr. Kathleen Sheerin, vice chairwoman of the public education committee for the American Academy of Allergy, Asthma and Immunology.
"This study is not saying if you take an antibiotic during pregnancy, you will have an allergic child," Sheerin says. "This study is an interesting observation, not fact."
If you are pregnant and have an infection, discuss it with your doctor, Sheerin advises. "Then take antibiotics for infections that call for antibiotics."
Sheerin uses the example of her own pregnancy. She had a urinary tract infection and took antibiotics to treat it. For her, she believes it was the right course of action because urinary tract infections can cause premature labor.
"You have to weigh the risk versus the benefit," she says.
What To Do
Read more about allergies and how to treat them at the American Academy of Allergy, Asthma and Immunology. Find out how allergens trigger an allergic reaction at How Stuff Works.