Researchers at Boston University looked at data on babies born with birth defects between 1993 and 2010.
The study suggests pregnant woman who used decongestants containing phenylephrine during their first trimester were eight times more at risk of having a baby with a heart defect.
Some decongestants were also linked to higher risks ear and stomach deformities.
Doctors say the risk translates to only about 2 in 1,000 chance the baby would have those defects.
