A review of studies has found those whose mothers were prescribed drugs to deal with acid reflux in pregnancy were more likely to be treated for asthma in childhood.
Experts stress the research is at a very early stage and is not conclusive, advising expectant mothers to continue to take any medication they need under the guidance of their doctor or nurse.
They say the association could be caused by a separate, linked factor and that further research is needed to determine whether the medicines also affect the health of children.
Heartburn is caused by stomach acid passing from the stomach back into the oesophagus, the tube that connects the stomach to the throat.
It is a very common condition in pregnancy because of hormonal changes and pressure on the stomach from the developing foetus.
Drugs called H2-receptor antagonists and proton pump inhibitors can help to block the acid reflux.
They are considered safe to use in pregnancy because they do not affect the development of the baby.
Researchers, led by the universities of Edinburgh and Tampere in Finland, reviewed eight previous studies that had examined health records involving more than 1.3 million children.
The team found that children born to mothers who had been prescribed acid-blocking drugs during pregnancy were at least a third more likely to have visited a doctor for symptoms of asthma.
The scientists say that advice for expectant mothers should not change based on the findings but further studies are needed.
Professor Aziz Sheikh, co-director of the Asthma UK Centre for Applied Research at the University of Edinburgh, said: “Our study reports an association between the onset of asthma in children and their mothers’ use of acid-suppressing medication during pregnancy.
“It is important to stress that this association does not prove that the medicines caused asthma in these children and further research is needed to better understand this link.”
Dr Samantha Walker, director of policy and research at Asthma UK, said: “The study points us towards something that needs further investigation, which is why we need to see more research carried out into the causes of asthma, a condition that affects 5.4 million people in the UK alone.”
The study is published in the Journal of Allergy and Clinical Immunology.