A Canadian study of almost 5,000 mothers found those who used SSRIs were also more likely to have premature and low birth weight babies.
However experts said women should not stop taking medication without expert advice.
The study is published in the American Journal of Obstetrics and Gynaecology.
The researchers, from the University of Ottawa, compared the health of babies born to 972 women taking SSRI anti-depressants with that of babies born to mothers who did not use anti-depressants.
SSRIs, or selective serotonin reuptake inhibitors work by increasing levels of the mood chemical serotonin in the brain. They include Prozac.
The researchers found women using the drugs were twice as likely to have a stillbirth. They were also almost twice as likely to have a low birth weight baby.
Almost 20% of women who used SSRIs gave birth prematurely, compared to 12% of those who did not use the drugs.
Babies born to women using SSRIs were also more likely to have seizures.
The researchers said women should be fully briefed about the potential risk of SSRIs before taking a decision about whether or not to use them.
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