Danish and US scientists found use of SSRIs in the first three months of pregnancy was linked to a 40% increased risk - but the results are preliminary.
Cardiac defects appeared to be 60% more likely when the women used SSRIs.
But the researchers stress the results, featured in Pulse magazine, do not mean women should stop taking the drugs.
The findings were presented an International Society for Pharmacoepidemiology conference.
Their use during pregnancy was linked to withdrawal symptoms in newborn babies in a study published in The Lancet earlier this year.
And doctors have been told not to prescribe them to children because of an increased risk of suicide.
In the latest study, focusing on 1,054 women who took SSRIs during pregnancy, scientists also found that use of the drugs late in pregnacy was associated with a 40% increased risk of premature birth.
And a second study of 377 cases of persistent pulmonary hypertension in babies found SSRI use late in pregnancy was linked a 5.5-fold increased risk.
"As with all medicines, antidepressants should only be taken in pregnancy if the expected benefit to the mother is thought to be greater than the risk to the foetus, and all drugs should be avoided in the first trimester if possible.
"People taking antidepressants should not stop them without seeking medical advice."
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